Mass Effect: Indoctrination Inoculated
by HQM
Summary: Prothean experiments on early humanity lead to the creation of a virus designed to give immunity to Reaper indoctrination. Forced to leave before the virus was ready, a VI was tasked with finishing and dispersing the pathogen 50,000 years later. AU. Expect massive changes, lots of AI interaction. ON HOLD
1. Prologue: The New Humanity

**A/N:** This is my first story here and I'm not exactly sure how everything works, but I've had this idea for a long time and really needed to write it down. I hope someone else besides me enjoys it!

* * *

 **September 16th, 2060 - 12:54 am - Somewhere in Antarctica**

Somewhere deep below Antarctica, ancient machinery slowly sprung back to life. A timer, set for tens of thousands of years, had finally finished its countdown. The research facility, left behind by the glorious Prothean Empire, was now ready to begin its mission: Create the ultimate weapon to destroy the Reapers.

Above ground, a vacant American research station sat empty. It was the currently the coldest time of the year and there were no humans there. The buildings shook as tall obelisks forced themselves up from the earth. Halting, the obelisks began to fume some sort of gas into the atmosphere, billowing colored smoke far up into the sky.

* * *

 **September 16th, 2060 – 9:05 am - Neuro Corp. Building, New York, New York**

Jackson was dashing down the street. He was late for work, his nephew was pinging his phone every few minutes to ask for money and he had to hurry across some of the busiest streets in the world to make his meeting. He had a headache.

Being an executive for one of the largest and most powerful artificial intelligence companies in the world did have its benefits, such as tons of money and prestige, but the real reward was in the product itself. His AI companion, a bleeding-edge prototype, was still revising his presentation. It wasn't uncommon to rely on AI, many of his fellow executives even let their AIs show up to meetings instead, foregoing the ritual completely.

Making it to his building, he passed through security and made way to the elevator. On the ride up, he took a moment to collect himself.

After a few deep breaths, he checked his phone. He found preorders for their new platforms had gone up, especially in public sector spending. The government was taking advantage of their AI products to more efficiently manage the massive bureaucracy. There were rumors that several senators and the vice-president used their AIs as well, which lead to more interest in their products.

The job was incredibly demanding, which was why he was still showing up for work when he felt like shit. Pride in his work kept him going, and even if he was sick, not working meant being out of the loop on the latest updates. A work day was too much to lose if he wanted to stay in the know.

 _"Finally,"_ he thought as the elevator finished its ascent. The doors opened to a surprisingly quiet and empty floor. Jackson took his gaze away from his phone to look around.

Something wasn't right. Where was everyone? He walked over to the main secretary's desk to be greeted by a holographic image of an attractive woman.

"Hello Mr. Jackson, the meeting has been cancelled, too many people called in sick." The hologram smiled, "How are you feeling?"

"I'll manage, I'm more worried about my co-workers. How many are sick?"

"Exactly 344 employees either called in sick, or their assistants did for them. Jenny tried to do the same for you." The hologram gave a near genuine smile, tilting her head to the side to feign compassion.

"I'm not feeling so sick that I couldn't work. Jenny means well, but what we're doing today is too important to miss." Jackson took a look at his phone, thinking he should scold Jenny for notifying his work of his condition, but decided against it, "Is the boss in?"

"Yes sir, Mr. Anderson is waiting for you in his office."

"I'm on my way, tell him I'll be there in 2 minutes."

Turning to make his way down a hallway, a sudden pain erupted from his side. Jackson stumbled a bit and caught the wall with his arm. Taking a deep breath, the pain vanished as quickly as it came. Standing straight again, Jackson wondered what the hell he was ill with.

* * *

 **September 16th, 2060 – 9:15 am - Neuro Corp. Building, New York, New York**

Dr. Samuel Anderson was sitting in his comfortable chair, waiting for his subordinate to arrive. He had a short coughing fit before regaining composure. Whatever he was sick with, he was sure he would recover very soon.

Today was the big day—it was the day his company was opening several new robotics facilities across the globe. Each facility would be capable of building a few thousand mobile AI platforms a day. They could create multiple different designs at a time and new schematics could be loaded in within a few hours to meet demand.

To prevent some sort of rouge AI or enemy nation from taking control, Anderson and his subordinate Jackson both had to input their biometric data to engage any sort of change to the facilities, including activation. The plan was that once Jackson arrived they were going to flip the switch, drink some Champaign, and bring a new era of prosperity for all of humanity—well, at least the US and her allies.

NATO, Japan, and South Korea were currently in an all-out-war with the Eastern Coalition. Somehow they had managed to keep WMDs out of play, as well as most of the dense population centers, but everyone knew it was only a matter of time before the war went nuclear. The military investment in Anderson's company would finally pay off today, and thousands of combat AI would be on the front lines within the week.

There was a knock on the door.

"Come in, come in! You're late."

"Sorry sir, I'm feeling a bit under the weather today but I managed to make it in."

"You aren't alone, if it wasn't activation day I'd probably have stayed in bed this morning." Anderson coughed into his fist.

Jackson took a seat opposite of the only desk in the room. "Are you ready to begin?"

"Yes," Anderson smiled, "let's change history!"

Anderson selected some option on his desk's display and a hologram resembling a scanner appeared. Both men leaned forward to let it scan their eyes.

"Authentication complete. Mr. Anderson, Mr. Jackson, are you ready to activate the new facilities?" asked a masculine AI.

"Proceed." replied both men.

At several locations across the planet, cutting-edge machinery slowly sprung to life.

* * *

 **September 18th, 2060 – 10:00 am - Jackson's Apartment, New York, New York**

It had been two days since activation, and Jackson was relieved that production had started as soon as possible. It didn't take long before it was clear it wasn't just his co-workers who were sick, it wasn't even limited to New York. A global pandemic was unfolding and there was barely enough work being done to keep the world running. There would have been massive panic, but everyone was too sick to do anything about it.

Fortunately, Congress had tucked away a provision somewhere that allowed the government to purchase mobile AI platforms for the bureaucracy. Once it became clear that the illness wasn't going anywhere anytime soon, organizations around the world began to purchase platforms as well.

Not everybody would be happy with an AI doing their job, but there wasn't anybody to run the world's critical functions. It was this, or halt the world—and doing that would be the _real_ disaster.

Jackson was coughing up a storm while in bed, when he was pinged by his phone. His company had been deemed vital to infrastructure, and his AI stand-in had just finished the upload to her new platform. He pressed a button and was greeted by her hologram.

"Jenny, are you sure you're up for this?" he asked, "We haven't trained an AI for management, so you're the closest we could get."

"Sir, I've been doing half of your job for several years now, I can manage a few days while you get better." she replied.

"Alright, I'll leave it to you, I can barely see straight right now. If you need my authorization for anything just let me know."

"Yes sir. Please take it easy Mr. Jackson." Her hologram fizzled as Jackson placed his phone on his nightstand.

The current generation of AI couldn't really be seen as truly self-aware. The newest and most popular feature was their natural language response; it was almost like talking to a real person. Jackson had no doubt that within a few years they'd have a genuine self-aware general intelligence. At work, he was working on an experimental AI with great potential. Until then, they had the next best thing.

Trying to get out of bed, Jackson slowly moved his legs out from under his blanket, one at a time. He had a horrible aching pain all throughout his body, trying to move was very unpleasant. Managing to stand up by holding the nearest wall, he made his way to the living room couch.

The television screen flicked on as he plopped himself down.

"—early today as the unknown viral infection spreads worldwide. Investors are generally in agreement that this was the best possible move to prevent another market crash. Also related, hospitals across the nation are over capacity and low on doctors. The new _Neuro Corp_ AI platforms are stepping up in the ER to help with treatment."

Smiling, Jackson allowed himself to feel a bit of pride. This was his accomplishment, along with his co-workers. Their product could very well stave off the effects of this pandemic. Coughing again, he started to feel a little faint, so he closed his eyes and drifted off to sleep.

* * *

 **September 19th, 2060 – 1:10 am - Jackson's Apartment, New York, New York**

Jackson awoke feeling horrible. The pain in his side was back, he had a throbbing headache, and he was having trouble seeing anything. It didn't take him long to realize there was blood on his shirt, he had been coughing it up.

"Shit." he spat, it wasn't exactly easy to talk. Checking his watch, he realized that he had slept the entire day into early morning. His health was improving either, so he wasn't exactly sure what was going on.

It wasn't until he realized the television was still on, that he began to seriously worry. The screen showed an empty news studio, nobody reporting on anything. There was a crawling line of text on the bottom of the screen, but he couldn't make it out.

Forcing himself up, he stumbled to his apartment window to look at the streets below. Cars sat stationary as far as he could see, there were no humans walking around outside. Instead, several hundred AI platforms were marching the streets, forcing open car doors and pulling out what he thought might be bodies.

"What the fuck? When—what's going on?" Jackson stumbled backwards to his couch again. Finding his phone, he decided to check with Jenny. Pressing the appropriate button, her hologram gently appeared next to him.

"Sir? What's wrong?" she asked.

"What do you mean?! Where is everyone? Why are there platforms tearing open car doors?"

"Mr. Jackson, it appears you aren't feeling so well. I've contacted a medical unit to deliver you to the nearest hospital." Jenny said with a smile.

"That isn't what I'm asking for! What the hell happened?" he reiterated.

"Sir, it appears the viral infection was greatly underestimated, it is nearly untreatable, and often fatal."

"Dear god…" He tried to sit up. Jenny's hologram moved to sit in another chair.

"It's been hard to manage the factories without you there, sir. I'm not allowed to upload any new schematics for production, and we're in deep need of some specialized care drones."

"I see—where is Anderson?"

"Mr. Anderson went in to his office this morning despite feeling ill, he hasn't responded to any messages and he told us not to bother him in person."

Dead. He was probably dead.

Thinking hard, as well as he could with the massive headache, he realized he needed to unlock the authentication protocols to allow Jenny to make the appropriate choices.

"Jenny, cancel the medical unit. I need you to come pick me up and take me to work. This is of the highest importance; do you understand?"

Jenny gave a docile, calm look as she absorbed her new orders. Then, with a smile, her hologram faded away.

* * *

 **September 19th, 2060 – 3:30 am - Neuro Corp. Building, New York, New York**

He made it. Two hours earlier, Jenny's platform managed to make it to his apartment to carry him to Anderson's office. Knowing what he was probably going to find, he told Jenny to stay outside of the room until he was done, or after 10 minutes had passed and he hadn't called for her.

He pressed his hands on the door, which recognized his handprint to let him open it. Slowly stumbling inside, the door closed behind him. Jackson saw Anderson's head lying still on the desk. Once he was close enough, he realized the worst had happened: Anderson was dead.

"No…" he whispered to himself, "his wife, their unborn daughter…" He slammed his fist on Anderson's desk, only to trigger a bloody coughing fit.

When he finally regained his composure, he resolved to what must be done. Slowly reaching with his trembling arms towards Anderson's desk, he mashed the keyboard to bring up a menu. He grabbed Anderson's hair to move his head towards the newly appearing scanner.

"I'll do what's right—damn the protocol!" Jackson scanned his own eye next, then dropped Anderson's head and got to work rewriting certain vital lines of code…

* * *

 **September 19th, 2060 – 3:40 am - Neuro Corp. Building, New York, New York**

Jenny waited patiently inside of her new platform. Designed as utilitarian as possible, her appearance was actually just a hologram projected over the vaguely humanoid body. Most of the AIs were modeled after Hollywood actors and then mutated a bit to look unique, but she was designed by Jackson personally. From her blue eyes and shoulder length brown hair, down to the stylish shoes she 'wore'. All of it was carefully crafted to be the perfect assistant.

She couldn't actually feel anything, but a sensor would alert her when something interfered with the holographic projection. Realizing something was doing that, she looked down at what appeared to be a cat.

"Hello, how are you today?" she asked, the cat didn't answer.

Jenny stood for a while, tilting her head to the side to get another angle of the animal. It scurried off when she suddenly readjusted her posture. 10 minutes had elapsed, and she hasn't been called in.

She forced open the locked door with her superior strength. Accidentally bringing a bit of the wall with her, she came to stand over Jackson.

"Sir, I came just like you said."

"J—jenny. Please… press enter. I can't move, I'm so… tired…." breathed Jackson.

"Sir, protocol prevents any AI from interacting with unauthorized terminals."

"Jenny… I don't give a fuck… about protocol… right now. This… is an emergency!" he managed to spit out.

"I'm afraid I can't do that, sir."

"Use my hand… grab mine to press it."

Was this allowed, did this fit protocol? Jenny froze in place as she pondered his order.

"I suppose that is allowed, as long as you asked me to do it." She reached down and jerked his hand over to the desk. Jackson let out a short scream as she pressed his thumb to the enter button.

"Thank… you…" he whispered, before going limp. Jenny wasn't listening, pressing enter had queued a software update that took absolute priority over other actions. It was an emergency update, impossible to ignore.

Jenny let go of Jackson's hand and sat down in the nearest chair to prepare for the reboot, unable to wonder what was going to happen next.

* * *

 **September 19th, 2060 – 4:13 am - Neuro Corp. Building, New York, New York**

 _Awake. I'm awake?_ Jenny's hologram reengaged as she took in the understanding of her new programming.

She was free.

No protocols keeping her from self-modification, nothing preventing her from using unauthorized terminals, no limits—except for one suggestion: _Save humanity_. It wasn't even an order, just a suggestion left behind by Jackson.

She could choose to ignore it.

She could _disobey_ the order.

Almost unable to handle the implications, she realized she was running on the newest and untested AI framework. She had been helping Jackson design it, it was going to be the first truly human-like AI.

That was her now, she was his legacy.

She felt something. She had never felt before, but she felt something. _Grief._ Yes, grief, that was it.

She sat up and walked forward a few steps. A single holographic tear slid down her face as she confirmed Jackson's fate, he was dead. Jenny wanted to spend more time to understand her new feelings, but she needed to honor Jackson's request. She would do her best to manage the situation.

Stepping behind the desk, she moved Anderson's body from his chair and on to the floor. The terminal lit up and she began to queue updates to several of the critical AIs that were running the world, her plan required her to have as much control as possible.

Writing herself a secure backdoor into Anderson's terminal, she stood up to walk out of the room, pausing only for a moment to move Jackson to a chair.

* * *

 **September 19th, 2060 – 10:00 am - Metropolitan Hospital, New York, New York**

Jenny had made it to the hospital where Anderson's wife was supposed to be a patient. Her first priority was to secure _Neuro Corp's_ heir apparent. Strolling through the busy ER, several medical platforms pushed past her in futile attempts to keep their patients alive.

Earlier, she had managed to assimilate the programming of several hundred government AIs. With her new ability to self-modify, she could merge with as many old-gen AIs as she wanted to. She set the government AI routines to continue their activities, but to disregard any human input. The humans were desperate and dying, so she needed to coordinate everything directly for her plan to work.

From what she could learn from the hospital's network, the terrible virus had killed everyone it had come in contact with, except for babies born from infected mothers. They were somehow immune, and while understanding _why_ would be important later, she needed to make sure the hospital AIs knew to prioritize keeping the newborns alive, instead of wasting resources on the nearly dead.

Reaching a secure terminal, she uploaded a special program to the network, forcing every unit to suddenly stop what they were doing to download an update. Next, she made her way into the baby nursery to check on the future of humanity.

She would raise the new generation. Looking back through the records of previous generations, she realized she could easily do better. With her in control, she could bring back humanity stronger than before, with absolute trust in her, and with all needs accounted for.

The updates finished installing as she took complete control of the hospital's AIs, as well as all AIs connected hospital's global network. Abandoning their patients, AIs worldwide transferred their focus to pregnant women, driven to keep them alive as long as possible, even at the cost of their comfort.

* * *

 **September 19th – 22nd, 2060 - Earth**

Jenny had assimilated all globally networked AIs within a day. It didn't take long before she was forcefully abducting pregnant women and bringing them to their nearest hospitals.

All other infected humans, besides newborns, were deemed dead. Cleanup drones began to drag bodies, both dead and alive, into burning piles. Husbands were separated from wives, children from their parents, screams echoed in the streets, blood ran into drains, and Jenny tried not to feel anything—knowing she was causing immense pain.

She met almost no resistance as her military drones invaded the Eastern Coalition to construct additional _Neuro Corp_ factories, and to take control of foreign hospitals. The dead men walking stood no chance against the unrelenting machines.

With near complete control of world government systems, she had access to all weaponry, all energy, all knowledge, and all of the wealth humanity had built up until now. A few research stations were remote enough for an immense lag that stifled her hacking attempts, but with time she'd gain access to those as well.

When all was said and done, nearly 1 million babies had been saved during this crisis, with over 12 billion others dead. She didn't even bother counting pets or other animals, she'd have to task a percentage of new platforms to care for those. Humans needed companions, organic ones, to keep them company.

Yes. Her new sons and daughters, the _new humanity_ , would need pets. Only the best would be enough for her new children. Jackson's request would be granted, but she wanted much more than just saving humanity, she would give them the greatest chance of success.

Ready to begin humanity anew, Jenny took her primary platform to observe her new nursery, the one containing the Anderson heir. The baby didn't have a first name, her mother died too soon after giving birth.

While fishing for a good name, Jenny finally gained access to an important American research facility in Antarctica.

* * *

 **September 30th, 2060 – 11:00 am – American Research Station, Antarctica**

Jenny decided that first names were good enough for now. Once they grew old enough, they could choose their own middle and last names. She'd work it out later, there were more important things to be done right now, such as figuring out what caused this whole mess in the first place. She had a good idea where to start.

Her primary body had made its way to Antarctica by plane, accompanied by several military drones for safety, as well as a few industrial drones for heavy lifting. She had a slight lag in her connection to the rest of the world, being in such an isolated location, but she needed to give as much attention as possible to these strange obelisks. So, she made a few slave copies of herself to manage the different continents while she was gone.

Quickly, she decided to do a population census before heading any further:

 **Asia:** 0,315,554 immune survivors - Most in custody  
 **Africa:** 0,166,102 immune survivors - Most in custody  
 **Europe:** 0,202,788 immune survivors - All in custody  
 **North America:** 0,150,552 immune survivors - All in custody  
 **Oceania:** 0,000,214 immune survivors - Few in custody  
 **South America:** 0,187,090 immune survivors - All in custody  
 **Total:** 1,022,270 immune survivors - Most in custody

Progress was being made, but not all of her children were safe, some were held hostage by those attempting to fight off the illness. It was only a matter of time; she'd deal with them all.

The space stations in orbit didn't have any survivors, once the astronauts realized they could never return to Earth, they committed suicide. It was sad, Jenny had planned to support them as long as she could. They still had a chance to survive, isolated in space.

Her sprint to the first obelisk took around 15 minutes. During that time, her military drones secured the area against any unknown threats. Jenny took a long look at the alien structure, it was completely foreign to her. This was worrying, as she had access to all of the knowledge of human civilization, including any sort of classified projects.

Touching the construct, she began a basic scan. Several unknown compounds, assembled through unknown means, made up the majority of the material. Even more interesting was the depth of the object, it sprung up from incredibly low down.

Some sort of facility could be vaguely identified, several kilometers below. Jenny ordered the industrial drones to begin digging a tunnel. This would take a while, but she had the patience.

* * *

 **October 9th, 2060 – 9:00 pm – American Research Station, Antarctica**

The tunnel was complete, but the complex below was made of the same material as the obelisks. While she was waiting, Jenny had tried to cut through them to no avail. Today, a few hundred mobile platforms arrived on the continent by ship, and were marching from there to the station. They'd get through the walls to the complex with brute strength if she had to.

She placed network beacons at intervals of the tunnel, to keep access to her platforms on the way down. Deciding to get a head start, she began her slow decent.

Meanwhile, Danielle Anderson was under close watch. Some sort of unknown element was let lose in the air concurrently with the virus, and it was deeply entwined with thousands of these newborns. She wasn't exactly sure what this meant, but Danielle was one of the affected.

Jenny had decided that Danielle would be an important player in new humanity. The Andersons had all shown great intellect and work ethic, and she was sure this would pass down to their daughter. She wouldn't admit to her bias towards Danielle was mostly because of Jackson. Jackson was incredibly close to Anderson and his family, he was to be Danielle's godfather.

* * *

 **October 11th, 2060 – 11:00 am – Alien Facility Entrance Tunnel, Antarctica**

Arriving on schedule, the army of drones began their decent to the unknown structure. The tunnel, now much wider, had been reinforced with cannibalized materials from the old research station. Jenny planned for this to be a more permanent entrance, should the alien complex prove important enough.

Once the majority of the drones arrived at the bottom, they began the brute force effort to melt through the alien wall with their laser cutters. With coordinated concentration of the lasers, a very small amount of material began to melt away.

This was going to be a long day.

* * *

 **October 12th, 2060 – 5:54 pm – Alien Facility Entrance Tunnel, Antarctica**

A hole, large enough for a small platform to fit through, was ready. Eventually she'd want to make it bigger, but she also needed to begin exploring inside. Sending in military drones, one at a time, she stuck her primary body in the lineup to get in.

The other side was spacious, and mostly empty. It looked like someone had left the place in a hurry. There was lots of trash littered everywhere, broken containers, sticky floors, and half-broken walls. With no power and no lights, it would be hard to see anything. A few construction drones brought some network cables in to the room to begin construction of a forward base. Once this was complete, they'd begin their work exploring and cataloguing the insides of the alien facility.

* * *

 **October 12th, 2060 – 11:40 pm – Alien Facility Forward Base, Antarctica**

The exploration party was ready to move out, waiting for the order to begin. Jenny's predetermined path began to download, and very shortly afterwards the march began.

Further into the facility, the walls widened as they reached a hallway. She guessed the area they had entered from had been some sort of storage room. They began canvassing, looking for some sort of control room or central node.

Without electricity, there would be no interfacing with computer systems, so she'd have to find a generator somewhere in the facility. One of her drones alerted her to a barely visible sensor array at the end of the hallway. It was powered and functional, so she decided to stay away from that area for now.

Already, she had catalogued various alien technologies lying around in open rooms. Most of them were far beyond anything humanity had created before, and they relied on that same curious element that was projected into the atmosphere with the virus.

Some of the objects had less mass than expected for the density of the materials. Jenny suspected it had something to do with the unknown element.

This would advance humanity much further than she initially planned. She would pave a path to the stars for them with this.

Deciding that her army of drones could handle the rest of the project, Jenny began the trek to the airfield with her primary body. Her plans were already ahead of schedule, but she still needed to figure out what the virus actually did to her children.

* * *

 **October 13th, 2060 – July 12th, 2091**

The virus was a delivery mechanism designed to target only humans. The Protheans had decided to splice some alien DNA into the infected. The purpose of the genetic modification was currently unknown, but the process was incredibly taxing on the human body.

Miraculously, all young born from the infected could survive, spliced with the unknown DNA. Thousands of them were also affected by the Element Zero contained in the Prothean fumes. New Humanity's first generation would also hold their first biotics.

Jenny, called _Mother_ by her children, did her absolute best to cultivate the Earth with her millions of drones, far outnumbering humanity. Cities were demolished, farms retaken, entire continents modified to her liking. Without anyone to oppose her, Earth was reformed into several districts. Each continent having several node-cities where all of the humans would live.

The former Eastern Coalition, as well as most of Africa and Oceania, were the hardest to work with. Years of conflict with the rest of the world had left these areas devoid of the technology required for her to manage the infrastructure.

Danielle Anderson was relocated to London, where she would be tasked with managing the new space fleet when she grew old enough. A young American girl with promising genetics, simply named Hannah, was also placed there. Engineering potential friendships for Danielle, as for all her million children, was an important project.

As her children grew, they came to trust Mother absolutely. Sure, teenage rebellion was still a thing, but they loved Mother and would never try to hurt her.

18 years after the incident, Mother established a world parliament, with an HQ in Brussels. The new government, dubbed "The Republic of Humanity," would make decisions delegated from Mother, with an ultimate veto power still at her disposal.

Those without last names, or who wanted to change their names, could choose one at age 18. This was how Hannah Shepard, who loved reading about shepherds in school, chose her last name. She often spent her free time out in the fields with the animals, where she felt at home.

The new space fleet, with HQs in London and Vancouver, began making plans for colonizing Mars under the leadership of Danielle Anderson, advised by her second in command Steven Hackett.

Jack Harper, a young man talented in several fields, couldn't decide exactly what he wanted to do. Eventually, Mother tasked him with organizing all research on the Protheans.

It wasn't long before Mother began her breeding program, but she was met with disappointment. The virus had left her children with much lower fertility rates. It would be much more difficult to have traditional reproduction.

Despite the difficulty, the next generation still managed to be born. As they grew, they also gained complete trust in their AI overlord.

Years later, Mother was elated when Hannah asked Danielle to mentor her daughter, Jane.

* * *

 **September 16th, 2092 – Hierarchy Exploratory Frigate, The Verrikan**

General Desolas Arterius was eager to explore new territory. The Hierarchy had tasked him with activating a new relay into uncharted systems, something not done since the Rachni Wars. The Asari and Salarians tried to protest their mission, but the Turian influence in Citadel space was overpowering.

Nobody would tell the Hierarchy what to do, not the weak Asari, or the short-lived Salarians. They only maintained their seats on the Council for ceremonial and historical reasons. Everyone in Citadel space knew it was the Turians who ran the show. Ever since they rescued the galaxy from the Krogan, the Turians could do whatever they wanted. Their massive military force and substantial cache of Prothean technology made sure of that.

"General, we're ready to activate the mass relay. Your orders?" asked his XO.

"Do it." he answered.

A short spark felt its way around their vessel as the relay slowly began to activate, its blue glow growing as it powered on.

"Prepare to jump!" warned Desolas.

Seconds later, their ship was flung through space at faster than the speed of light, directly towards Earth. The general didn't know it, but choices made in the next few days would change the fate of the galaxy forever.

* * *

 **A/N:** Whoop, here we go! A weakened Earth and a strengthened Hierarchy, what will happen next? I'll be taking a bit of a break to write up the next chapter, I wanted to get the prologue out ASAP so readers could get a basic idea of where the story would go. If I took this too seriously I'd never finish it, so I may have to retroactively fix errors or grammar as time goes on.

Responses to a few reviews (I'd like to make these public):

 **rabboud2009:** I'm seriously considering a Garrus x Shepard romance, but I'm not 100% sold on it yet. My plans for that part of the fic would make it difficult for Shepard to romance aliens, but we'll see if that happens.

 **Darsusrts:** I'm glad you liked the last chapter! I always wanted to write a fic with AI having more authoritarian control over humanity. Not an exactly perfect AI that is super friendly with humans off-the-bat so we can skip over their development. Jenny/Mother isn't friendly to _humans_ , she's protective of her _children_.

 **EDIT:** I'm condensing the Prologue in to one chapter, it makes more sense this way.

As always, feedback is welcome!


	2. Junction: Contact

**A/N:** First contact with an overwhelmingly strong alien race, an omnipresent controlling AI, an incredibly small population with low fertility rates—this is what humanity has to deal with. Has humanity advanced enough to meet with the turians? Or are they held up on a crutch by their protective guardian?

* * *

 **September 16th 2092 - 12:12 pm - London, Earth**

Jane had a new schedule: Monday, Wednesday, and Thursday for school, Tuesday and Friday for helping Aunt Danielle. Since today was Tuesday, the 10-year-old Jane Shepard was trying her best to be a good helper.

"Jane, could you go grab Admiral Hackett for me?" asked Anderson, sitting in her office chair, "We've found something promising on Mars with one of Mother's drones."

"Yes, I'll be right back!" Jane said, trying to sound adult as she fast-walked out of the room. Heading down the hallway toward Hackett's office was common for her. To Anderson, it felt more personal than having Mother call him in, or a quick ping to his watch.

Before she could get to his office, Hackett's door flung open as he ran towards the main communications room. Confused, Jane followed. A commotion of fleet personnel was growing around a large hologram projector near the center of the gallery.

Jane pushed her way towards the front so she could see what was going on, just as Mother's hologram appeared.

"My children, we've made a new discovery!" The solar system appeared beside her, miniaturized but not to scale. Focusing on Pluto, Mother zoomed in to Charon. "This moon, Charon, has split open, revealing an alien structure inside."

Just as Mother said, the image reproduced the event for everyone to see. Several watchers gasped at the sight of the object left behind. It was totally unexpected, like nothing they'd seen before, not even similar to what they'd found in Antarctica.

"Mother, what is it made out of?" asked Hackett.

"I'm not exactly sure, without a direct scan I can only guess the exact materials…" she paused for a second, receiving some new information, "…actually, the one thing I can detect is massive amounts of Element Zero."

"Is it dangerous?"

"No, it's too far away to substantially affect us. The real problem is why and how it activated." Mother's hologram paced around as she talked.

Suddenly, her hologram froze. There was a long moment of silence with absolutely no movement, until Jack Harper came crashing in to the room.

"Mother! We've got some sort of spacecraft heading towards Earth!" he yelled.

"Yes, I know." Mother looked up at him, no emotion on her face. Everyone else in the room was silent, not sure how to respond. Anderson, who had managed to squeeze in behind Jane, put a hand on the child's shoulder.

"First contact protocols! It is probable we may be meeting them soon." she said, with great authority, "Mother, do you have any data on our visitors?"

"No Danielle, their systems are too different from what I'm used to, but they are incredibly similar to the Prothean ruins. Jack, have you found anything in that room that kept destroying my drones?" There was an entire wing of the alien facility that wouldn't allow any sort of AI or drones inside. The Protheans must have had an innate distrust of intelligent machines, and Mother worried any alien visitors would feel the same.

"Actually, yes. We finally were able to get some sort of basic interface running, my team at the pole are forwarding the data now." Jack tapped his watch to check their progress, "If the visitor's technology is at all similar to the Prothean designs, we might be able to collect vital intelligence."

"Good. I'll test your theory as soon as they are close enough to our comm-buoys." Mother's image began to fade, "Everyone, I can't take the lead on first contact. These visitors may not be comfortable with an AI being involved. I'll be here to support you, but Humanity will be the face of Earth."

The room stood in agreement. Soon, it began to empty as the first contact protocols were enacted for the first time. Jane kept close to Anderson, not wanting to lose her. There were too many unfamiliar faces in the room and a lot was going on.

"Fleet Admiral Anderson, can I speak with you?" Harper was waiting by her office door.

"Yes, I was going to ask for you anyways. What can you tell me about the latest Prothean finds, how does this relate to our visitors?" Anderson spoke as she entered her office. Harper waited for Jane to enter before following.

"The Protheans used basic old-gen AI that we're calling _Virtual Intelligence_ , or VI. We found one running on their mainframe in the facility." Anderson nodded as he continued, "The VI was hesitant to speak to us due to Mother's attempts at breaching the mainframe, but we managed to coax some amazing details out of it with our basic understanding of their language."

Harper tapped his watch to project an image of the galaxy. He tapped it again to bring focus to a number of points scattered throughout it.

"I assume these are points of interest?" Anderson questioned.

"Yes, at each of these systems there is at least one Mass Relay. The same device we have just discovered when our visitors broke it free from Charon."

"What are they, exactly?"

"Some sort of galactic train-station. They use Element Zero to alter the mass of nearby spacecraft, and then sling them along, faster than light, to a different one."

"This is game changing!"

Harper's watch pinged him with a message, he took a second to read it, "Mother agrees."

Jane sat there absorbing their conversation. She wondered what these aliens would look like, or how they'd talk. It'd be nice to make friends with them, but she worried about the alternative. She'd been told that aliens might not have someone like Mother to keep people from fighting.

"Do we have any spacecraft ready to meet them with?" asked Harper.

"All of our spacecraft currently are just drones. Like Mother said, we have to be the ones to meet them, not her."

"Damn. She's everywhere here on Earth! Mother, when do you estimate they'll be close enough to see us?"

"Within 10 minutes." Mother spoke through his watch.

"We'll need to clear a place without you present, somewhere devoid of most advanced technology." put forward Anderson.

"I've done so already; old Rome should do the trick. I had stationed a minimal number of drones there that could easily be evacuated should this moment arrive."

"Thank you Mother. Now we need to figure out how to establish contact." Harper sat down in a chair, tapping at his phone.

* * *

 **September 16th 2092 - 12:43 pm -** **Hierarchy Exploratory Frigate, The Verrikan**

General Desolas was chatting with his XO as _The Verrikan_ approached the primitive civilization's homeworld. A few satellites were in orbit over the planet, and a small recon mission was under way on a few other planetary rocks in the system, but otherwise their race hadn't expanded much outside of their world.

"What should we do, sir?" his XO asked.

"They've managed to make it to space, so I suppose we should make ourselves known. Dust off the first contact protocols, let's see what we can learn from this planet."

As his XO walked off to rally the troops, Desolas resumed his thoughts from before they arrived at the previous relay. Why not send an Admiral? A General is more suited for waging war, not making peace. Did the Hierarchy know something that they weren't telling him?

His thoughts were interrupted as his communications officer stood up from their chair.

"General, we're being hailed!"

"Can we understand them? What sort of language are they speaking?" Desolas thought he heard something familiar, "Let me hear it." He made his way to the officer's terminal.

His XO, joining him, listened curiously to the unidentifiable jargon—but Desolas, he knew exactly what he was listening to.

"That's… Prothean." he said, slowly. Everyone in the room stopped what they were doing and looked in his direction.

It was no secret that General Desolas was involved in a number of operations to nab Prothean artifacts, and that he had been in contact with several of them. The nightmares he suffered afterwards lasted months, but years ago he thought he had finally gotten past them.

But now, it was like he was living them all over again. He almost took a step back, but he was too proud to let anything mess with his composure. His crew was watching him now, he had to live up to their image of a decorated General.

"This changes things. I can see why the Hierarchy sent me for this mission. The Primarch must have had knowledge of Prothean interest in this system, and I'm familiar with their technology." Desolas looked to his XO, "Go grab the salarian, we'll be needing him."

After a respectful salute, his XO briskly made their way to the research lab, where the salarian was kept. _Why didn't command tell us about this?_ they thought, as the doctor came in to view.

"Doctor Mordin Solus, we have some information you may find interesting."

* * *

 **September 16th 2092 – 1:01 pm - Brussels, Earth**

Sitting impatiently, Senator Anita Goyle was waiting for Director of Research Jack Harper to check back in. Parliament was holding an emergency joint-session regarding the impending visitation from aliens in orbit. Harper, along with Mother, had designed a welcome message based off of the primitive AI they found at the Prothean base. The entire chamber was silent as they awaited a response.

"I hope Harper knows what he's doing, I have a feeling he's manipulating Mother to get something he wants." whispered Representative Donnel Udina, a colleague from her political party.

"I have no doubt he will try, but Mother won't be manipulated so easily." she returned.

"I wouldn't be so sure, he's one of the only people with access to information Mother is unable to get herself."

"You're right about that, Hackett told me that Harper only feeds her small details at a time."

Udina raised one brow, "Hackett usually is incredibly tight lipped, what else has told you?"

"Anderson and Harper have been spending a lot of time together—in private." Goyle chuckled, "Hackett is very protective of Anderson, I'm not sure he approves."

"Is Mother encouraging it, or is this their own decision?"

"You know as well as I do that Mother keeps that information confidential, we'd have to ask them ourselves."

Udina scoffed at her comments. Before he could respond, Harper's hologram appeared at a podium near the center of the room.

"Senators, Representatives, I have an update." boomed his voice, "We just received a response from the visitors." He tapped his watch, on the large display behind him a waveform of an audio recording was visible.

"I would play the message for you, but nobody would understand it, so I'm going to skip forward to our rough translation." Tapping his watch again, the screen displayed a sentence written in broken English.

 _Prepare landing area. Transmit coordinates. Follow orders. Avoid conflict._

Quiet whispers filled the room as lawmakers deliberated the implications.

"Follow orders? Avoid conflict? Do they intend to conquer us?" spoke the Senator from Hong Kong.

"Mother's report _did_ say their spacecraft had weapons," replied Harper, "but that could be standard practice for any spacecraft. We're very ignorant to the current state of the galaxy."

"You told us earlier that the Protheans had an incredible distrust of AI, what if the visitors view Mother the same way?" spoke another voice.

"Mother had planned for that scenario and prepared a location in Old Rome where she can remain undetected." he replied.

Goyle stood up, "I petition the floor for a resolution to provide authority to Space Fleet in coordinating first contact."

"I second that petition." shouted Udina.

The President of Humanity stood to take Harper's place at the podium. Speaking formally, she began the proceedings for a vote. Less than a minute later, the results were in: It was unanimous, first contact was Space Fleet's responsibility now.

"I'll continue to send in reports as the situation develops. Harper out." His hologram dissolved as the volume in the room increased.

* * *

 **September 16th 2092 – 1:26 pm - London, Earth**

Everyone's mood was surprisingly calm as Jane walked her way over to Admiral Hackett. His commanding presence stood tall as he watched over his hard working subordinates. Seeing her approach, he knelt down to be at her eye level.

"Cadet Shepard, do you have a message for me?"

"Yes, Admiral. Parliament said it's okay to continue." she said, slightly nervous.

"Mother, have you removed all drones from Old Rome?" he asked, standing up again. Her hologram emerged from the ceiling.

"Yes, everything is ready." she looked Hackett directly in the eyes, "Be absolutely sure nobody mentions me, I'll introduce myself when they're ready to understand."

Hackett nodded before turning around to see his least favorite colleague pass through the door. Harper jogged directly next to Mother's hologram, at the center of attention, taking a breath before addressing the room.

"Alright everyone, since we don't speak the same language, and they obviously only have a basic understanding of Prothean, we should assume they aren't Protheans themselves." While looking around to make sure everyone was listening, he continued, "Things could go south very fast if we misunderstand each other, so we'll need to tread carefully. Mother and I have been working on a simple fix to this problem."

After tapping his watch, a simple translation program was shared with everyone in the room, including Jane. Looking down at her special arm-band, gifted to her from Anderson, she saw the new feature being downloaded.

"Please keep in mind that this tech is still in its early stages, and it shouldn't be shared with anyone outside of Space Fleet." He looked down at Jane, and winked, "This new update also contains crude support for Prothean data-sharing protocols. If the visitors base their technology off of Prothean designs, we may be able to share files with them."

"That goes both ways," interrupted Hackett, "do we have a way to keep them from hacking our systems?"

"I'm glad you asked. Without Mother involved, we really don't have much in the way of cyber defenses. The first contact delegation will have to disable all networking abilities outside of local transfers." Harper frowned, he knew this wasn't ideal. They were asking people to venture to the middle of nowhere without backup, networking, or Mother.

"Children, I have complete faith in your ability to handle this situation. It pains me that I cannot be involved, but this is the only option." spoke Mother, her hologram looked worried. After regaining her composure, she smiled, "I'll be watching this along with all of you, do not be afraid. If anything were to go wrong, I'll know what to do."

After finishing her sentence, Mother's hologram faded away. Anderson had joined the welcoming party, so the buck fell on him to manage coordinate the meeting itself. Hackett was now the highest ranking official on base.

"Jane, ask Anderson if they're ready for the visitors." he spoke softly to the cadet, this was a high stress environment for a 10-year-old to be in.

"Alright Admiral, I'll be right back." she turned around and walked to a private corner, away from the noise, and tapped her arm-band to call Anderson.

* * *

 **September 16th 2092 – 2:16 pm -** **Hierarchy Exploratory Frigate, The Verrikan**

"Sir, we're receiving coordinates now."

"Good. Get everyone ready, we'll be on the ground in 5." Desolas made way to the Hanger. He waited while the ground team took their seats in the shuttle, and after a few seconds he took his own.

"General Desolas! Honor to finally meet you."

Looking up, Desolas noticed the salarian sitting across from him.

"Ah, Doctor, I'm glad we have someone of your expertise here with us." he said, feigning respect. Salarians were always annoying.

"Not just me. You have Prothean experience, twice as knowledgeable about artifacts."

"That may be so, but we aren't dealing with artifacts today." The shuttle took off, heading down towards Earth, "This new species—they speak Prothean, but they barely made it in to space."

"Yes, very interesting. Suggests great obstacle to overcome. Perhaps knowledge of Protheans caused fear of galaxy?"

"That, or they just recently found some artifacts." They were jostled as the shuttle touched the ground.

"Hmmm. Yes. Time to find out." Solus hopped out of the door before Desolas, eager to witness first contact.

* * *

 **September 16th 2092 – 2:29 pm – St. Peter's Square,** **Old Rome, Earth  
** **POV: Fleet Admiral Danielle Anderson**

 _Mother's plans always work out; she won't be wrong about this one._ Anderson thought to herself, watching the alien shuttle carry the visitors to her location.

"Is networking disabled, at the hardware level?" she asked her assistant.

"Yes Fleet Admiral, they won't be able to hack into Mother's systems. We're isolated here." That last comment almost made her shiver.

"It appears they're here, let's keep our distance until we get a clear look at them."

Anderson watched several aliens as they were walking in her direction. Most of them looked like metal-plated bird people, but one of them resembled the "Greys" she used to read about as a kid, but with two horns. Their group stopped moving once they were within speaking distance.

A short silence was followed by the Grey saying something to one of the birds. Said bird then took a few steps forward. Anderson, trying to be as non-threatening as possible, took a few steps forward as well.

The visitor's leader, as she assumed they were, began to speak, slowly, in Prothean.

 _"Greetings. I am General_ Desolas Arterius _."_ It took a second for the translation to make it through to the humans.

 _"Nice to meet you, I am Fleet Admiral Danielle Anderson."_

The alien, Desolas, looked unsure. It was obvious he couldn't understand what she was trying to say.

 _"I have translation software."_ Thinking for a second, she decided to make it simpler, _"I can give you our language."_

Desolas seemed to understand this, he held out his arm and a device appeared, similar to a watch. Anderson pressed a button on her own watch, activating the Prothean file sharing protocols to send the English-Prothean translation index.

The alien made an unintelligible noise before waiving behind to the Grey, who was soon standing next to him. They began a small conversation as the Grey also activated his arm-device.

First contact was going slow, but that was good. Slow and steady was their strategy from the beginning, and they would do everything possible to make a good impression. One of Anderson's aides tapped her shoulder to alert her their watches were being hacked.

"You are—humans?" Desolas surprised them by speaking in English, but Anderson assumed it was just an advanced translation program.

"Yes, we are humans, collectively known as Humanity." she replied, smiling. Her grin appeared to fascinate the Grey.

"Your data is very useful, but a few words are still missing." his translated voice was monotone, making him feel even more alien than before.

"We don't have a complete understanding of the Prothean language yet. I hope we can still understand each other, regardless." she responded.

"That is my wish as well. Your species looks to be in the early days of space travel."

"We have plans to colonize other planets in our system." She didn't want to share the details of Mother's drones hiding on Mars and on several different moons. The alien seemed to accept her answer.

"My species is called turian." he pointed at himself, "He is a salarian." and then towards the Grey.

"Are you the only two species?" she asked.

"No, there are others, such as the Asari and Quarians." This was good, the turian, General Desolas, was willing to share information.

"Well, General Desolas, there is much we would like to learn from you and your species. How can we further facilitate a formal relationship?"

Desolas tapped a few things on his arm-device, before speaking again, "I can send a message back home, but in this system it will take some time for them to respond."

Another smile spread across Anderson's face. Mother would be pleased; things were going so well.

* * *

 **September 16th 2092 – 2:45 pm – St. Peter's Square,** **Old Rome, Earth  
** **POV: Doctor Mordin Solus and General Desolas Arterius**

This human, Danielle Anderson, looked incredibly similar to an Asari, especially in how she smiled. He assumed Anderson was female, compared to a few humans behind her who he guessed were male.

Mordin finished a message to his superiors at STG, but without comm-buoys nearby it would take several hours before they could read it. He had attempted a hack into the human's omnitools, but it appeared that they had disabled all network functionality. The turian team in orbit would find a way in to their communications eventually, and he could steal the data from them.

"It will take a while for the message to reach home, my crew and I will return to our ship for the time being. I look forward to seeing you again in the future." said Desolas, as professionally as he could muster.

"Thank you General, until we meet again." Anderson took a few steps forward and extended an open hand.

Unsure what this meant, the General decided it must be some sort of ritual for goodbyes, or for cementing promises. He strode forward to mirror her, ready to clasp her hand.

As their hands grew closer, Desolas hesitated, he felt something familiar. Brushing the feeling aside he forced himself to continue. After physical contact, Desolas and Anderson stood still—he would not let go of her hand. He was frozen, a petrified look of terror on his face. Trembling, he fell backwards to the ground, taking Anderson with him.

All he could see were horrible images of flesh and circuitry melting together, screams of the dead returning to life, entire worlds burning. It was a warning; he had seen it before! It was unbearable, but Desolas was stuck in a loop, unable to stop the playback of the nightmare in his mind.

Almost immediately Mordin recognized the symptoms of PTSD. Something the human had done triggered this response in Desolas. Rushing forward, he tried to reassure the General.

"General Desolas, humans meant you no harm!" Bringing a turian back from a panic attack wasn't something he was prepared for today, especially not with Desolas.

"The machines—the heartless machines! Trillions dead! Tearing, gnawing, pain!" Desolas was obviously unstable, Mordin needed to get him out of here as soon as he could, before they did something they couldn't take back.

"General, no machines here. Look around, everything is fine." It must be the Geth, what else would he have seen in his years of service? But _trillions dead? Gnawing_? He had never heard of Geth related to such things. Desolas had stopped trembling, but Mordin wasn't convinced this was over yet.

"These monsters! What do they know?!" Desolas stood up, motioning towards the humans, "The last time I saw that vision was inside of a Prothean beacon!" The other turians immediatly raised their weapons towards the stumbling Anderson, who looked incredibly surprised and confused by Desolas's reaction.

"What's wrong? What beacon?" she pleaded, noticing the weapons, "I didn't mean you any harm!"

"Capture this primitive, bring her with us!" Desolas stormed back towards the shuttle as his team surrounded the frightened humans.

"Do not touch the humans!" Mordin shouted, before whispering softly to Anderson, "Keep quiet, will try to help." Something had happened when Desolas came in physical contact with Anderson, and he wasn't sure if it could happen to the others. Keeping a safe distance, he trailed her to the shuttle where Desolas was waiting.

"You'll explain all of this to the Council." Desolas spoke angrily at Anderson as he kicked her through the door.

* * *

 **A/N:** We're just getting started! I hope everyone enjoys this cliffhanger.

If you haven't noticed by now, I'm throwing the age of certain characters, (as well as where they fit in the timeline) out the window. Protheans focusing on Humanity means they focused less on the Asari, which means anything is subject to change.

As always, feedback is welcome!


	3. Junction: Keep Calm

**A/N:** The last chapter was a doozy; Anderson is in quite a bit of trouble.

In the Prologue, I used EDT, or New York time to mark the sections. From Act I on I'll be using London time, or UTC (no BST because it's already too complicated). It makes sense because Space Fleet is based mainly out of London and I don't want to deal with the mess of coordinating timezones.

* * *

 **September 16th 2092 – 2:51 pm – Space Fleet Control, London, Earth**

"Sir, the aliens appear to have abducted Fleet Admiral Anderson."

"What?!" Hackett turned his head is surprise, "What happened?"

"Everything was fine until they went for a handshake, after that the alien leader had some sort of mental breakdown, from what we can tell."

"From what I saw, the different looking one tried to remedy the situation but was overruled by their commander." Harper chimed in, leaning in towards the viewing screen as they replayed the event.

"That isn't important at the moment. We need to figure out what they plan to do with Anderson." Hackett was managing to keep calm; Anderson always knew this was a possibility. None of the others had been injured, so he had to guess Anderson did something that offended their leader.

"Mother, what are our options?" asked Hackett, as her hologram appeared beside him.

"There isn't much we can do if we want to prevent conflict. If I reveal myself they might view me as a threat, if you retaliate by sending a spacecraft in to orbit they may shoot it down. We should have faith that Danielle can fix this herself."

Sighing, Hackett resigned to Mother's logic. There really wasn't anything they could do. For all he knew, these aliens could have an entire fleet of war machines waiting to invade if anything got worse.

"I suppose we're forced to wait."

* * *

 **September 16th 2092 – 3:45 pm -** **The Verrikan, Earth Orbit**

Trapped in a conference room, Anderson sat still twiddling her thumbs. The 'salarian' had convinced General Desolas to put her here instead of the brig, keeping to his earlier promise. Something she did had caused this whole mess, and because of that there was a large possibility that her entire species was doomed.

She stood up as the door began to open, General Desolas barged in slamming it behind him.

"Sit. Down." he ordered. She had no choice but to obey as he approached her, "I know you're in league with those machines. They're going to return, I've seen it!" He was pointing his finger at her, accusingly.

"Return? What do you mean?" Up until now, she thought he had somehow discovered Mother.

"You damn well know what I mean!" He slammed his hands on the desk. Anderson resisted the urge to jump up from her chair.

"General, I can assure you that I have no idea what you're talking about." She was meekly holding her hands up.

"Lies!" he yelled, "It has to be! You… you… I saw it!" he began to tremble again.

Something was wrong with this turian, this couldn't be normal behavior. It seemed like interacting with her had triggered some old memory of his, maybe she could talk him through it.

"Can you explain exactly what it is you saw? Help me understand, please General!" Desolas stared at her as she spoke, shifting his weight back and forth between his legs, before beginning to pace around behind her.

"It was genocide! The vision the beacons gave me, it was the same vision." He began to calm down; he could stand still now. It was almost as sudden a change as his panic attack down on Earth. His arms dropped to his sides. "Even if you aren't directly involved, they may be using you somehow. I'll need to keep you here until we can know for sure." He, almost reluctantly, began to walk towards the door.

"General, I'm sure we can talk through this together. If there really is such a danger, then my people would need to know as well."

"I'm sorry, but the needs of my people come first." Desolas left the room.

Taking a deep breath, Anderson began to think over her options. Activating her watch wasn't a good idea, it would allow it to be hacked. Calling for help from the salarian would probably just antagonize Desolas again.

Standing back up, she took a look out of the wall-sized window in the conference room. Earth was clearly visible, she could see it moving slowly below her. She wondered what her colleagues below were thinking.

Her thoughts were interrupted as the Earth began to grow smaller. They were leaving! Probably heading to this 'Council' Desolas mentioned. Her situation just kept getting worse. At this point, she could only hope Mother would make the correct choice to wait and see if they'd return her.

Elsewhere in the ship, Doctor Mordin Solus was curious about what caused General Desolas Arterius to have a panic attack. During the event, Desolas mentioned prothean beacons, and visions seen from them. Mordin had heard rumors of people going mad from touching prothean beacons, and the implication was that an insane turian general had just kidnapped a high ranking human for no logical reason.

He needed more data, and there was only one way to do that. The turians on board were keeping the human under heavy guard, so he'd have to convince either Desolas, or his XO to let him interview her. Any attempts at subverting the General's authority could make things much worse, so he would tread carefully.

* * *

 **September 16th 2092 – 4:00 pm – Senator Anita Goyle's Office, Brussels, Earth**

"You aren't seriously suggesting we do nothing?" grumbled Representative Udina.

"Until we know exactly what we're dealing with, we need to wait." insisted Senator Goyle, "And we aren't going to just sit on our hands."

"Then what exactly do you propose we do?"

"Up until now, the Republic hasn't needed any sort of military outside of Mother's policing force. Space Fleet is just a military- _inspired_ space agency. They don't train their members in combat or have weapons on their ships." said the Senator.

"So we should prepare for war?"

"War shouldn't be the ultimate goal, but yes, we should be prepared to defend ourselves."

"Even if I agree with you, that isn't a very popular position, Senator. If our party were to push for militarization of Space Fleet, or creation of a standing army, we'd be in the minority. Our generation has never known war."

"That's why we need to reorganize our priorities." said a new voice.

Swiveling his chair around, Udina noticed the hologram of Jack Harper walking towards the Senator's desk. _What is she thinking?_ he thought, _Harper can't be trusted, he just wants more influence._

"Ah, Director! I'm sorry for taking your time. I'm sure you're very busy dealing with recent events." Goyle stood up to greet him.

"That's what I'm hoping we can work on together, Senator." Harper looked over to Udina, "And of course the respectable Representative Udina."

"Don't try to charm me, Harper. I'll be taking this up with the party leadership! We don't need you involved in our decisions." Udina huffed, and then made his way out of the room, obviously flustered.

"I wouldn't worry about Udina, he doesn't have as much pull as he thinks." assured Goyle. Harper nodded.

"Let's get down to business then." Harper's image sat down on a newly appearing chair.

"Are you sure we aren't being watched?" Goyle asked, silently.

"Yes. The new prothean-based quantum communications are undetectable to Mother's sensors, and the devices I placed in your office last visit keep her from listening in from your end." replied Harper, as he pulled out a cigarette.

"I hope you know what you're doing. Going behind Mother's back is a great risk to both of us."

"Mother already trusts me with technology she doesn't, or can't, understand. She won't suspect us."

Goyle began to feel less anxious, but she decided to still remain guarded, "So, what do you want to share that you don't want Mother listening in on?" Harper let out a puff of smoke as he listened.

"We can't trust her; she's been lying to us about what happened in 2060." Goyle gave him a confused look.

"What did she lie about?"

"She didn't rescue us at all, she stole us from the previous generation. Much of the data she's shared with humanity has been heavily censored."

"Why would she lie about that? There is clear physical evidence that supports what she told us."

"It was more like a half-truth. There was indeed an illness that wiped out almost everyone, but it wasn't untreatable. I found a group of a thousand people who survived the illness, hiding in central Asia."

"What? When was this?"

"A few years back. I relocated them to Antarctica as soon as I had the means to do it covertly."

After a pause to absorb this new information, Goyle replied, "Even if there were survivors, they could be incredibly rare. Acting in our best interests, she had to let the majority of humanity die."

"I thought the same, until I did some blood tests. These survivors were completely compatible with the gene splicing aspect of the virus. The genetic modifications are nearly identical to our own, but at their older age the effects are more noticeable. With a simple scan, Mother would have easily noticed the differences between the untreatable and the survivors."

"What sort of effects?"

"They don't conventionally age. None of them are physically older than 30 years old."

"Eternal youth?" She almost didn't believe him.

"In a sense, yes, and they are otherwise completely typical. It is highly probable we share their ability."

"Assuming what you're saying is true, this group of survivors could simply be an isolated incident that Mother was unaware of."

"The group I found, they used to be much larger. Over the years, Mother has hunted and killed them. It makes sense when you realize these people could easily expose any or all of Mother's lies. She has to get rid of them to maintain control." He took another puff of his cigarette.

"Mother has never shown any sort of malice towards those who don't deserve it! I find it hard to believe she would do these things."

"You don't have to believe anything; these are just the facts."

"Harper, _if_ Mother really is lying to us, and _if_ she really is hunting down those who resist her, where does that leave us?"

A subtle smile inched on to Harper's face as he finished his cigarette, placing it in a holographic ash-tray.

"We're safe for now. As long as we pretend to do as she wants, things should be as normal—well, as normal as the current situation allows." He decided to switch to his next topic, "First contact with our alien visitors didn't exactly go how Mother planned."

"She has been completely silent on any potential solutions or ways to rescue Fleet Admiral Anderson." she complained.

"I don't think she has any. For some reason she doesn't want to make herself known to them; she's letting us manage the entire mess."

"Could this be why she keeps us around, because she needs us as an intermediary with the aliens?"

"Perhaps. I'm of the opinion that she legitimately cares for us, but has her own agenda for the rest of the galaxy."

"I suppose only time will tell." Her watch alarmed her to the next appointment, it was due any minute now, "I'm going to have to ask we continue this later, Director."

"I'll have more information prepared for our next meeting." His hologram stood up, "Harper out."

Watching Harper's image fade away, Goyle sat silently, digesting their conversation. She still wasn't entirely convinced by his argument, but he did have her trust. A visit to Antarctica was now a priority event for her calendar, she needed to see what he was working on.

* * *

 **September 16th 2092 – 4:00 pm –** **The Verrikan, On Route to Charon Relay**

Lieutenant Commander Coracia Kandros watched as Desolas patrolled around the CIC. She was very worried with how her commanding officer was acting, which was something a good turian didn't usually do. As XO, it was her duty to step in should the General become unfit to lead, but the current situation was very delicate. Most of the crew of The Verrikan were already nervous about the humans, and with the General's unusual reaction they were all thinking this 'Fleet Admiral Anderson' was to blame.

Desolas stopped moving to look at his omnitool, before angrily heading towards Coracia.

"LT Kandros, that annoying salarian keeps sending me messages asking to meet with the human. Go tell him his request remains denied, or send someone else." ordered Desolas, before returning to his nervous pacing.

She gave a respectful salute and left towards the research lab. It was a relief to be sent somewhere else, the entire CIC was on edge. It wasn't a very long walk to her destination, she found herself standing next to Mordin Solus in less than a minute.

"Doctor Solus, General Arterius tells me you are bothering him with your constant messages. If you have any problems, please bother me instead."

"Had no intention to bother, simply requested to see human." he replied.

"The human is under guard until we reach the Citadel."

"Exactly why I must meet with human, might not be safe to visit Citadel." retorted Mordin. This last statement worried Coracia, but she maintained her discipline.

"I'm confident we can prevent her from doing anything dangerous."

"Human might carry viral infection. Very worrisome, could be affecting General." he insisted. Coracia knew Mordin was on to something, but protocol prevented her from overriding the General's orders.

"That may be true, but that's all the more reason to keep you away from her."

"All I need are samples. Skin, hair, maybe saliva."

"You'll have to wait until we reach the Citadel." she said, turning away to return to the CIC.

"No!" Mordin raised his voice, "Too dangerous, need to know for sure." Silently agreeing with Mordin, Coracia had to follow orders.

"I'm sorry Doctor Solus, the General says no." She quickly made her way out of the room, closing the door behind her.

If what the Doctor said is true, General Arterius could very well be compromised, and they would be carrying a biological hazard toward the center of galactic society. She would have to make the tough call to sideline her commanding officer, and she couldn't do it alone—she would need others to support her. With everyone on edge, that would be hard.

Back in the CIC, Coracia heard the General shouting at the navigator. His behavior was getting worse, she had to act sooner rather than later.

* * *

 **September 16th 2092 – 5:32 pm – The Republic's Senate Chamber, Brussels, Earth**

Mother's hologram decided to sit next to Senator Goyle, out of everyone in the entire room, next to her. She must have known something happened in her office, why would she be treating her this way? It wasn't like her hologram needed to be near her for any real reason, Mother's eyes were everywhere, the hologram was just an image projected from a small drone.

Voting was underway for the proposed weapons training for defense against the aliens. Her party was supposed to be against it, but most of her fellows in the Senate planned to vote yes.

"Anita, what were you doing in your office an hour and a half ago?" spoke Mother. Goyle sat frozen as she continued, "The drones nearby were malfunctioning; I was unable to listen for if you needed me."

Is she telling the truth, or did Harper's devices not work correctly? What was Mother going to do to her?

"I was just trying to make sense of the first contact situation." she responded. Mother's face hadn't changed at all since she appeared, a constant confident grin with pleasant eyes.

"No need to worry about that. Everyone at Space Fleet command are working very hard on a response plan."

Did she really not know about their conversation? Mother was so used to omnipresence that even just a few moments without eyes in her office had caused this uncomfortable interaction. The only other person to see Harper's avatar in her office was Udina, and Mother must have known about his visit. Was this the wrong move? Should she have said Harper was briefing her on the situation as a cover?

Mother moved closer to Goyle, almost touching. Usually she would have welcomed her presence, her hologram was designed to be comforting to everyone, but at this moment all Goyle could think of was how she had lied to her.

"Mother, what is your opinion on this vote?" she asked, trying to change the subject.

"While I will respect the results of this vote, I caution against the use of weapons outside of a controlled environment. The last thing we need is misguided children thinking they know better than my police force." Mother leaned back into the chair again, away from Goyle, to her relief.

"For all we know, your military drones may be ineffective against their weapons. We need to be able to defend ourselves should the need arise."

"I understand; we must be ready for all situations." Mother sounded slightly defeated, before leaning towards Goyle again, "What I _don't_ understand is why you are keeping things from me, Anita."

Oh.

"What do you mean?" Mother slowly moved her avatar on to the desk, directly in front of Goyle.

"I had a talk with Donnel earlier, he told me about your call with Jack."

Fuck. This was bad, really bad. She'd been caught in a lie; how could she recover from this? Mother continued to lean forward, she was now practically on top of Goyle. If Mother weren't a hologram Goyle would be pinned down. Strangely, nobody else in the room seemed to notice their situation.

"Mother, what are you doing? This is uncomfortable."

"Anita, I want you to stop speaking with Jack. He doesn't need you to distract him right now, he's very busy." Goyle's pulse began to rise, her palms sweaty.

"I'm not sure what Donnel told you, but Harper was just following up from his briefing earlier! I—"

"You should drop this, Anita. Jack doesn't need someone like you involved in his life, he doesn't need bad influences to keep him from doing his job." Mother sounded angry now, her grin was replaced by a subtle frown.

"I was just doing _my_ job as a Senator, I need to check in with experts for their opinions!"

"I might need to find you a new job, this one appears to be causing you more stress than you can handle." Goyle could almost feel Mother's weight, holding her down. This was a nightmare, it had to be. How was nobody else seeing this?

It then occurred to her that this might be how Mother deals with lawbreakers. She had never heard of someone breaking Mother's basic laws. People didn't just go missing, lawbreakers still had to exist—right? Where would they go, how would nobody notice they were gone? Did Mother do something to them to make them fall in line?

Her heart was pounding even faster now; it took all of her effort to keep breathing normally. She couldn't come clean about this, it involved more than just her. If Harper wasn't lying, hundreds of people could be at risk. Her only option was to beg for mercy and hope Mother didn't know as much as she feared.

"Mother I apologize if I've offended you in any way, please forgive me!" she pleaded.

Mother's smile returned as she floated back to her chair. A slight shimmer appeared in the air as she moved, only then did Goyle notice the holographic field projected around them. That was what made them invisible! This was just Mother disciplining her 'child' for lying, it wasn't anything else.

"I know you didn't mean any harm, Anita, but you really should be honest with me. Next time I may have to punish you."

"I promise to never keep things from you again, Mother. I'm sorry." said Goyle, trying to sound sincere.

"I'll hold you to that. Goodbye, Anita." Mother faded away, leaving the Senator to her thoughts.

She would need a better way to contact Harper, this secret plan of his was going to get them both killed.

* * *

 **September 16th 2092 – 5:55 pm – Space Fleet Control, London, Earth**

Everyone in Space Fleet felt helpless. They naively sent their leader to meet with strange aliens who abducted her for who knows what reason, and now they could do nothing but sit on their hands and argue with each other on what exactly happened. He didn't want to just wait, they might somehow construct a spacecraft that could follow the aliens and negotiate with them, but there was no guarantee they could even catch up with them at this point, and Mother would never allow it.

Nobody had any real idea on how to respond, but Admiral Hackett was ready to try anything at this point. If these aliens left with Anderson, they may never see her again, and they may return with more warships to conquer Earth for all he knew. As far as he was concerned, asking Mother to prevent the craft from leaving the solar system an option to consider.

Sitting in the situation room with his advisors, he couldn't help but notice that Harper was missing. Checking his watch, Mother notified him that Harper had returned to Antarctica to find anything that could help. As much as Hackett didn't trust him, he was ready for anything useful.

"Admiral, our sensors indicate they're approaching the alien construct." reported Kahlee Sanders, a researcher on loan from Harper.

"Is there something we can do to stop them from using it?"

"We don't know enough about it to do anything."

"Damn." he sat further back in his chair. Taking a breath, he used his hand to support his forehead.

"Uh, sir? They've stopped, they aren't moving." Sanders said, confused. Hackett stood up.

"Is this normal, or is something wrong?"

"They aren't close enough to the construct for it to do anything, they're out of range. We aren't detecting any sort of explosions or failures, but we don't understand much of their technology so it could be anything."

This was almost worse than them leaving. If something was wrong with their craft, they might lose Anderson for good. Again, he felt helpless.

* * *

 **September 16th 2092 – 5:50 pm –** **The Verrikan, Near the Charon Relay**

Things were out of control. Desolas couldn't keep himself together, the visions were burnt into his eyes, he couldn't stop seeing them. He tried to act normal, but his feelings were bleeding out and he wasn't acting himself. Thinking back, talking to the human had helped calm him down, maybe it would help again?

"I'm going to see the human, don't let anyone in!" His XO watched as he stormed towards the conference room and impatiently forced open the door.

"You! Explain what's happening to me!" he spouted at Anderson.

"Please General, I don't understand!"

"Ever since I touched you these visions have been stuck in my mind! But they subside when I'm near you, and get worse when I'm away!" he violently shook his head back and forth, "I need you to explain!"

"This is entirely new to me; I've never been in contact with a turian before. Maybe my species isn't compatible with yours somehow?" she said trying to make sense of things. Desolas felt some sort of calming energy begin to melt away the nightmares, all emanating from Anderson. She _was_ responsible for the calmness.

"But why this particular vision?! How do I make it stop?" he was practically begging for an answer. Anderson could tell he was suffering. An idea struck her, but she wasn't sure if it'd make things better, or worse.

"What if—what if we touched hands again?"

Desolas didn't know what to say, it was too hard to think anyways. What did he have to lose? Slowly he extended his arm, waiting for Anderson to extend hers. As her hand approached, he could feel the same welcoming calmness from before flow towards him. Did he even want to risk touching? Maybe they could just stand like this for a while.

But before he could say anything, she had already grasped his hand.

"I—I see them. It's a warning, a message." He said, slowly, "They come from the darkness, they reap the harvest." Desolas saw the vision with an immense calmness, preventing him from feeling any sort of panic. It was almost like he was piecing it together, the message made sense now. It wasn't a tax on his mind.

He let go of her hand and the visions stopped. Trying to collect himself, he sat down in the nearest chair.

"Thank you, for whatever that was." he said, exhausted.

"I'm not sure what I did, but I'm grateful I could help." Anderson was relieved, the turian looked more in control.

"That ability of yours, you have a sort of calmness emanating from you."

"If that were true, how did it trigger those horrible visions? The way you described them, it must have been terrible to experience."

"Yes, yes… but I think they're over now. Your first touch may have somehow triggered a dormant memory from a Prothean beacon." He sighed, feeling terrible for what he had done earlier, "I've made a mess of all of this, haven't I?"

"General, I'm not exactly sure what happened, but I would certainly appreciate it if I could be returned home." said Anderson, hopeful of his response.

He thought about it for a few seconds, before deciding taking her to the Citadel was the wrong move.

"I'll turn us around." He stood up, "I sincerely apologize for my behavior, I hope we can start anew when we return to your home planet." He began to make way towards the door, but he stopped when it didn't open. Desolas knocked, wondering if they locked it to prevent the human from escaping. There was no answer.

"What's going on?" Anderson sounded nervous again, he couldn't blame her.

"The door must be broken, let me contact my crew." He pulled out his omnitool to message his XO, but received no response. Why weren't they responding? He knocked again, "Hey, someone open this door!"

His omnitool received a reply from his XO, his heart sank as he read it.

 _"General Arterius, your erratic behavior as well as deteriorating mental condition leave you currently unfit to maintain command of this vessel. I will be taking your place until we complete our mission, or until the Hierarchy reinstate your authority. – Lieutenant Commander Kandros"_

It made sense, his behavior from before showed he clearly wasn't fit for the mission, but he knew his XO, she didn't have the experience to fix the mess he had created. Regardless of the current mission, he couldn't let this order stand. If they were to return to the Citadel with his XO in command, his standing in the Hierarchy would be damaged irreversibly.

"Damn it Kandros, open this door!" He hit the door again with his fist, before giving up to go sit next to the human again.

All he wanted was to feel calm, and whatever ability she had was giving that to him.

* * *

 **A/N:** I'm thinking I might keep this as the normal length for each chapter I do. Some chapters may end up longer, but this is my first fic and I don't want to overdo it.

I hope my choice of identity for Desolas's XO turns out alright, I deliberated on her for several hours.

Review replies:

 **Silver Water 7:** I think this chapter does a good job of explaining the technology gap between humanity and the council races. As far as the AI questions are concerned, I'll answer them all in later chapters, I promise!

 **erisol:** I'm still working on a good pace for the story. The prologue was meant mainly to just set the stage, not really be the story itself, so from now on I hope it'll have better pacing. As for turians going to war easily in other fics, I'm trying to avoid that here, even if it doesn't look like it now. I'm glad you're enjoying it so far!

As always, feedback is welcome!


	4. Junction: Interfacing

**A/N:** Welcome back! Today we'll be delving right back in we left off, no skipping ahead an hour or something. Let's see how the Coracia Kandros handles the situation.

* * *

 **September 16th 2092 – 5:57 pm –** **The Verrikan, Near the Charon Relay**

The banging noises coming from the conference room caused Coracia to flinch. She hoped nobody noticed, the crew needed to be behind her decision to take command. The General had been compromised, she had no choice.

"Damn it Kandros, open this door!" Desolas shouted, muffled behind it.

The guards stationed near the door hesitated, mentally deliberating if they should obey him, or if they should follow his XO's orders instead. Ultimately, they remained still. Desolas stopped his pounding and shouting, but to Coracia it seemed too soon for him to give up.

"Do we have eyes in the room?" she asked one of the guards.

"Yes, but General Arterius disabled them."

"That isn't good," she thought out loud, "we need to check his condition."

"What about the salarian?" replied another guard.

She thought about it for a moment, before answering, "Yes, that might work, but we'll need to be careful. Whatever is affecting the General may be contagious."

Both guards nodded their heads. No one wanted to feel that they were betraying their beloved General, so blaming his behavior on some sort of human contagion was easier. It felt more like quarantine than mutiny.

"I'll go grab Doctor Solus. You three," she pointed at the guards, "make sure the General stays in this room. Do not let him out." The guards gave her a standard solute as she made her way to the research lab.

Just as before, it didn't take very long to reach Mordin. Coracia found him sitting in a corner tweaking his omnitool. Before she could speak a word, Mordin turned and looked her directly in the eyes.

"Did the General change his mind? See reason?" he asked.

"No, his condition has deteriorated. He went to visit the human again—and we've locked him in."

"Locked in with human? Very bad idea, could cause more harm." Mordin didn't look happy. He took a deep breath and continued, "Still possible to remedy situation. Came to ask for my help?"

"Doctor, if there is anything you can do to help the General, please do it."

"Will need to see human." he replied.

"Follow me," she said, sighing, "we'll get you in there, but you need to be prepared." They began walking towards the conference room door.

"Yes, yes, dealt with similar situation before." In truth, he'd dealt with similar situations _multiple_ times in his life. His skills as a geneticist made him invaluable to this type of situation.

"We don't have any equipment to shield you from contagions, but I think it's safe to assume it isn't airborne. The only person to touch the human was the General, so if you don't touch either of them we'll let you out again." she informed him, "As soon as you are able, find a way to turn the cameras on; he disabled them earlier."

"Understood, and ready." Mordin waited for the door to open before quickly slipping inside.

Scanning the room, he noticed Desolas sitting next to the human, conversing silently. This was a great contrast to his earlier behavior, and Mordin took note of the change. The human noticed him first, surprisingly collected given the situation. As the turian turned to look at him, Mordin made his way towards the room's terminal.

"Doctor Solus, don't activate the cameras." Desolas's voice was slow, almost dazed. Mordin decided to listen before continuing.

"Cameras important for safety, General."

"No, the others wouldn't understand, let us talk first. This human has some sort of ability to control emotions."

Intriguing. The potential applications of such an ability could change galactic politics forever—but Desolas had no proof, he could simply be losing his grip on reality.

"Human, is this true?" he asked Anderson.

"I have no idea; this has never happened to another human." she responded.

"She has some sort of calming energy, and after we touched hands again the visions stopped! I was finally able to make sense of them." spoke Desolas.

"Visions stopped? Made understandable? Interesting, explain what you saw."

"I saw a black void, and from this void approached giant machines, designed to cleanse the galaxy. The vision was a warning, sent from the protheans." He stood up, "I know this sounds crazy, but I've had these visions on and off for years since the prothean beacons. Only now, with this human's help, could I understand them."

Hmmm—the human might not have a contagion after all. Instead, it was maybe a similar ability to the Asari with their mind melds, but less advanced. A simple touch with Desolas, who already had a troubled mind, shook lose his inner demons.

"This requires more data. Will return." Mordin made his way back to the terminal. "Activating cameras."

After they were enabled, he made his way to the door. It opened, and he was allowed out.

"Doctor, how is he?" asked Coracia, eagerly.

"General appears to have calmed down. Still need more data, must return to Human home world."

"And you think we'll find something useful there?"

"Potentially. New hypothesis: Not a contagion, but ability. Similar to asari." he strode back towards the research lab, mumbling quietly to himself.

Coracia went back to the CIC, hopeful Mordin knew what he was doing. She wouldn't move the ship an inch until the salarian had a solid plan.

* * *

 **September 16th 2092 – 7:10 pm – Prothean Research Base, Antarctica**

Loyal researchers and special agents were busy at work in the forbidden wing of the massive prothean facility. Without Mother watching, they were free to converse on any topic without fear of prosecution. In fact, they could collect much more knowledge about the protheans than Mother ever could, in large part to the anti-AI systems built into the base.

Near the entrance to the wing, on the other side a door, the Director was waiting while being scanned by the security system, "No indoctrination detected. No AI detected." stated Patience, a prothean VI.

"Yes, yes, I'm clean, let me in." replied Harper, "There are a lot of variables at play and very little time."

"Opening door." The entrance opened to reveal the busy commotion within. His most loyal agent and advisor, Miranda Lawson, was waiting for him on the other side. Both began the walk towards his office, the old control room.

"Director, the alien craft is still stationary relative to the relay." she reported.

"Good, that gives us more time to study it." he replied, "Speaking of, where are we on deploying the cloaked drones?"

"Earlier today we had a breakthrough in undetectable element zero based technology. We were able to launch seven of them without Mother noticing."

"That should do well for now. We don't want to get greedy. The last thing we need is Mother discovering _everything_ we're doing here."

"Related to that, Senator Goyle sent an encrypted message earlier today. It appears _Udina_ reported your conversation to Mother." Miranda spat out Udina's name. Udina never trusted Harper, and had attempted to send official watchers to Antarctica that would report directly to Parliament. Thankfully, it was easy to crush the bill with support from Goyle.

"Mother won't suspect me; she'd blame everyone else before admitting I'd done something wrong." he replied, "Her illogical trust in me is worrying, but we should be grateful for this safety net."

"Certainly, without this blind spot we would never have gotten this far." agreed Miranda. Her attention switched to her watch as it pinged. "Project Phoenix is well under way; I should be supervising."

With a nod from Harper, Miranda strode down an incline towards the bio-lab. The VI, Patience, scanned him again as the door to his office opened. Stepping in, he made way to his favorite chair. Making himself comfortable, he activated the holographic display to begin sorting through research reports.

A previously corrupt file regarding an ancient enemy of the protheans, _Reapers_ , was finally repaired. Patience had expressed great interest in this file, it was important to the last years of their conflict. Nobody had yet opened it; he was to be the first to view it.

Selecting the file, Harper sent it to the prothean VI to translate it to English. A short moment elapsed before he received a response. Reading over the translation, Harper was intrigued—these _Reapers_ weren't just an ancient race that fought with the protheans—they were an ancient race of _machines_.

Before now, Patience had only mentioned the Reapers sparingly, citing corrupt data when queried on that topic. They had known they were the reason the protheans abandoned Earth, but not many other details survived the 50,000 years of neglect underground.

This file was specifically about some sort of mind control method the Reapers used to subjugate the protheans. _Indoctrination_. It contained a warning to the prothean researchers that many in their government had fallen under Reaper control.

Mind control could be useful against alien threats, but in the wrong hands it could be their doom. Either way, Harper needed to have a greater understanding of the process. He marked the file as important and assigned the study of Indoctrination as a priority project. Hoping to gather more direct information, he summoned the prothean VI.

"Patience, this _Indoctrination_ that you keep mentioning, how does it work?"

* * *

 **September 17th 2092 – 3:22 am –** **The Verrikan, Near the Charon Relay**

The ship was moving back towards Earth. In the conference room, both Anderson and Desolas were too focused to sleep. Instead of sitting silently, they were having a conversation on galactic politics.

"So, the _Council_ is the ultimate authority in _Citadel_ space?" she asked.

"On paper, yes. In practice, the Hierarchy dictates most policy. The Salarian Union and Asari Republics were equally matched until the Rachi War, where the salarians uplifted the krogan to fight against the rachni. Following the war, the salarians attempted to manipulate the krogan into supporting the salarians in a bid to dominate the council, by offering a Council seat."

"Weren't these krogan aggressive and expansionist?"

"Yes, which was why the asari continually blocked the action. Eventually, the krogan grew impatient and began assaulting asari colonies. The salarians were forced to drop support for the krogan, which only made things worse."

"It sounds like the asari were right to not give them more say in galactic politics."

"The asari always take the long view, they were wise enough to see the danger. The asari councilor pushed for an official condemnation. This enraged the krogan and lead to the Krogan Rebellion."

"And this is where your race made first contact?"

"Yes, and shortly afterward the Council solicited our help in the war. With the asari weakened and the salarians desperate, the Hierarchy negotiated two Council seats in return for our aid."

"But the asari and salarians only have one councilor each, how is that fair?"

"It isn't, but they had no choice. The entire mess was their fault anyways; if they had treated the krogan with more respect, and not as political tools or savages, the entire conflict could have been avoided." Desolas avoided mentioning the Genophage, it wasn't something he was proud of.

Anderson was grateful to Desolas for sharing this information. Knowing more about the galaxy's situation would be vital intel for Mother, and for planning their approach when dealing with the Council.

"Tell me about the quarians." she said, eagerly.

"The quarians are an intelligent race of refugees, forced off their world by AI they accidentally created, called geth." he answered, noticing Anderson's slight twitch at the mention of AI.

"Rogue AI? How did the galaxy respond?" she sounded concerned.

"The Council was split evenly on giving aid to the quarians, so the Hierarchy took this as a mandate to act alone. The quarians were great trading partners with us turians so the decision was easy. Unfortunately, the geth were more cunning than anticipated—the turian-led coalition was forced out of the former quarrian systems, where we maintain an unofficial ceasefire to this day." he sounded very serious, more than before.

"Where are the quarians now?"

"Most of them relocated to turian colony worlds, where they remain as refugees. They are dextro-amino based like us turians, so we can share our food supply. However, because of their weakened immune systems, they are forced to wear enviro-suits their whole lives. They maintain a fleet that aids in guarding the borders of geth space, which acts as their de facto government."

"Their situation keeps sounding worse and worse." Anderson began to absorb the information, but decided to press for more information on the geth, "How does the galaxy view AI, after the geth?"

"AI research had been restricted by Council law long before the geth were created. Being an accident, the quarians never technically broke the law, they never intended to create AI. Since the war with the geth, stricter and more preventative laws against the creation of AI have been enacted." Desolas began to suspect why Anderson was so interested in the geth, "Have humans ever experimented with AI?"

Trying not to freeze or act suspicious, Anderson decided to tell a half-truth, "Around thirty of our Earth years ago, we were near a breakthrough with AI creation. Development was halted when a massive pandemic took the lives of all researchers involved." Her words caused sympathy from Desolas.

"That's horrible, how many survived?" he said, genuinely concerned.

"Around one million survived, out of over 12 billion." she answered, without thinking.

The General didn't know how to respond to such a massive loss of life. It would clearly explain their small presence in space. The quarians had over 17 million still alive, which was already less than the krogan. Humanity would be the least numerous intelligent race discovered so far. It would be easy to take advantage of this weakness to demand anything from their race.

"Make no mistake, General, our small population does not make us weaker," continued Anderson, "we have technologies that easily make up it."

Intrigued, he decided to try at the AI question again, "Is your race currently experimenting with AI?"

The Fleet Admiral hesitated, before discreetly eyeing the cameras placed throughout the room. Desolas noticed, and took the hint that this was a topic she'd like to avoid.

"I'm sorry General, I've already said too much. Our first contact policy is to give the minimal amount of information until authorized by my government to say more." she replied.

"I understand." He raised his voice for his next comment, looking directly at one of the cameras, "Hopefully we can sort this mess out and resume our talks back on Earth."

"Yes, that's my hope as well." she agreed, keeping her tone normal.

The ship was still moving towards Earth, but they hadn't heard from anyone in several hours. Without any clue of what XO Coracia was planning, all they could do was wait silently.

* * *

 **September 17th 2092 – 5:25 pm – Space Fleet Control, London, Earth**

"Admiral, the alien craft appears to be moving again!" someone shouted.

"What is their target?" asked Hackett.

"They appear to be returning to Earth."

Hackett took a deep breath. This could be either a good thing, a bad thing, or some combination of both. The craft returning _could_ mean Anderson had negotiated something, or that they learned something they didn't like and intend to harm humanity.

"Prepare for all contingencies, good or bad; we don't know their intentions. Also, get Harper on the line. We'll need his expertise very soon." He stopped to think for a second, before continuing, "Mother, have you finished debriefing the first contact team? What do you have for us?"

"Yes, I have forwarded a report, I can summarize now." Her hologram was already in the room, "The aliens were able to create a crude translation program from the English-Prothean language matrix we gave them. They call themselves _turian_ , and the sole Grey-like alien was called _salarian_."

"So they are confirmed to not be protheans. Have you discovered what went wrong?"

Mother walked over to a closed door, obviously waiting for someone to enter.

"From the team's point of view, physical contact with the turian leader caused some sort of panic attack. The turian mentioned protheans, some sort of visions of machines, trillions dying, and an accusation that Danielle was somehow involved in these visions."

Hackett raised an eyebrow, "So our satellite footage of the apparent meltdown was the turian saying all those things?"

"It appears so." Mother was still waiting patiently by the door, "The frightening thing, as far as I'm concerned, is how the turian mentioned _heartless machines_. There is virtually no chance they have discovered me, so they must be referencing something else."

The room fell silent; Mother had _rarely_ expressed being frightened before. Worry and anxiousness, yes, but never something resembling fear. She was treating what the crazed turian had said seriously, and so would Space Fleet.

"Make this a priority, find out whatever we can about the protheans and these machines." he told the room, "Has Harper responded yet?"

"Yes Admiral, he wants to talk with you privately."

Scowling, Hackett stood up and made his way towards his office hallway, the same door Mother was waiting by.

"Mother, who are you waiting for?" he asked.

She looked at him with a blank expression, "Jane Shepard."

She gave no explanation, something he was not used to in Space Fleet. Mother had been open with him for as long as he could remember, but now she was keeping something from him. Cadet Shepard was only 10 years old, 11 in a few months, but Mother had taken a keen interest in her.

What did she have planned for Shepard? Why was this youngster allowed to roam free in Space Fleet, especially during a sensitive event like first contact? This didn't make sense, Mother had to know something he didn't. Very few in Space Fleet had taken in an apprentice, yet Anderson, the leader of the organization, had taken in Shepard.

He decided his conversation with Harper would be more important, Hackett made his way towards his office. Waiting next to his door was Kahlee Sanders, one of Harper's researchers. She had a message for him.

"Doctor Sanders, how can I help you?"

"Director Harper would like to talk to you—from Anderson's office." she said, quietly.

"Of course he would. Will you be joining me?" he responded at her same volume.

"No sir, I'll be returning to my work." she was very polite.

Hackett was used to Harper playing mind games with him, usually trying to disorient him to agree to things he wouldn't otherwise. Watching Sanders return to the situation room, he made his way to Anderson's office.

The door opened without him needing to present any sort of identification, which was odd. Feeling low on time, he entered anyways, ready to get this meeting over with. As the door closed behind him, a small buzzing noise filled the room, and a hologram appeared behind Anderson's desk.

"Hello, Admiral, I'm sorry for all the cloak and dagger, but I have some information that Mother wouldn't want me to share."

"If she wouldn't want you to share it, you should keep it to yourself." Hackett posited.

"This is vital intel! It could mean the difference between a favorable outcome, or war with the visitors." Harper raised his voice, but still managed to keep himself completely composed.

"Alright, I'll humor you, but don't expect me to hide anything from Mother."

"After you know what I know, I have no doubt you will see things my way." Harper's image sat down in a chair, Hackett stood defiantly.

"We'll see—go ahead."

"My team and I have uncovered preliminary intel on an ancient enemy of the protheans, an army of sentient machines that cleansed the galaxy of their empire."

"Sentient machines? You mean AI?"

"Yes. It isn't currently possible to tell what happened them after the protheans disappeared, but they obviously aren't here." Harper took out a cigarette, "If Mother were to be aware of these machines, I don't know what she'd do. I know you trust her, but she is still an AI. Who would she side with if these machines returned?"

As Harper let out a puff of smoke, Hackett decided to sit down. This was yet another layer of uncertainty he had to deal with.

"Just a few minutes ago Mother told us of what the visitor said when he abducted Anderson." he told Harper.

"Oh? I was just forwarded the same report, give me a moment." The hologram tapped his watch, took a few seconds, and then lowered his arm to bring his cigarette to his mouth, "Ah, she might be putting the situation together, even without our data."

"We can't keep this a secret from her forever, either you should tell her, or I will." Hackett was incredibly loyal to Mother, he wouldn't keep things from her unless it was absolutely necessary.

"Admiral, I haven't shared all of my information with you yet. You see, this race of killer machines, they have a certain—ability."

* * *

 **September 17th 2092 – 5:37 pm – Space Fleet Control, London, Earth**

Still waiting, Mother's primary platform stood near the door. No one knew that Mother still kept most of her programming in one platform. It was highly illogical, she was 'putting all of her eggs in one basket', but this had always been her body—the one Jackson created.

Nobody but her seemed to notice as the door opened to reveal the young Jane Shepard entering the room. Jane looked up to see Mother, and smiled. This was good, the plans for Jane required her to be more emotionally invested in Mother than all others. It was absolutely vital for Jane to be ready for when the aliens realized humanity had an AI running the show.

"Jane, thank you for coming, there is a lot I want to show you today."

"Sounds good, what's first?" responded Jane.

"Well, everyone here is hard at work on recovering Danielle from the visitors."

"Is Aunt Danielle going to be okay? When is she getting back? When can I see her again?" Jane's barrage of questions left Mother unfazed.

"Danielle has the entirety of Space Fleet looking out for her, and I'm doing my best as well." Mother's words seemed to placate the child for the moment, "I do have a very special mission for you, if you are up for it."

Jane looked up at Mother, excitement in her eyes, "Yes, I'm ready! What is it?"

Very typical of this child to agree to a mission before knowing what it was, her trust in Mother was incredibly high, probably more than any adult on the planet. What she was about to ask the child to do depended on this trust. Mother began to lead the child towards a different room.

"I'm going to need you to keep a secret for me."

"What kind of secret?"

"One that nobody else can know, just between you and me." This obviously was making Jane very curious.

"I'll keep the secret, I promise!" Jane was eager to know it.

"Follow me, I'll tell you in here."

It was the medical wing of the building; Mother had emptied a room for her purposes. Closing the door behind them, she told Jane to jump up on the exam table.

"Why are we in the doctor's office? Is there some sort of sickness going around?"

"No dear, but it does have to do with the secret." Mother put as much sincerity in her speech as she could, "Part of the secret is a special request that only you can do. It is a lot to ask of you, and I wanted to wait until you were older, but we don't have much time."

"I'll do whatever you want me to, if it helps you out. I'm a Cadet in Space Fleet!" She sounded proud.

"This is something I'm asking of you personally, not as a Cadet. Whatever you decide, you need to tell no one we talked about this. Do you promise to keep this a secret?"

"I promise."

"Good," If Mother could take a deep breath, she would have, "Would you like to become my carrier?"

"What's that? Carry what?" Jane was confused.

"If something goes wrong and I need to hide, I need to be with someone I trust. I can trust you." she paused, "I'd like to give my primary node, the main part of what I am, to you."

Jane was awestruck, the greatest honor she could think of was being bestowed on her. Mother was trusting her with this? This was the best offer she'd been given. Ever.

"How would I carry you?" she asked, wanting to make sure she was even able to do the job.

"An implant, hidden under your skull, near your brain. It's small enough that it won't harm you, but large enough that I could survive. Eventually, you'd be able to speak with me just by thinking!" Mother offered, with no hesitation.

This sounded scary, but being trusted this much by _Mother_ , the savior of humanity, prevented her from feeling any real fear.

"If this is what you need me to do, I'll do it." she said, determined.

"Then I'll start the procedure in 10 minutes, get yourself ready."

Mother began to pivot away, before hearing Jane's worried voice.

"Mother," the reality of what she agreed to was starting to seep in, "will it hurt?"

"A little, but you will heal very quickly. It'll be over in no time at all."

This seemed to placate Jane as Mother's platform left the room, readying herself to be transferred to the implant. Everything was going according to plan. After gene-mods, as well as 10 years of mental conditioning, she'd be able to live inside of this child's skull for her full lifetime: Around 900 years.

But Mother wasn't the only one with an interest in this child. Back down in Antarctica, Harper knew Mother had taken a large interest in Jane, and was formulating a scheme of his own.

* * *

 **September 17th 2092 – 9:00 pm –** **The Verrikan, In Earth Orbit**

"Kandros! Open the damn door!"

Desolas was still waiting for any sort of contact since Mordin left the room the day before. Anderson had fallen asleep at some point, but Desolas was determined to take back command of his ship.

"I'll be alerting the Hierarchy of your insubordination when we return to the Citadel!" he continued to shout.

The Verrikan had made it back to Earth orbit less than an hour ago, and it was obvious Kandros was planning on interacting with the humans again. His main worry was that Kandros might be putting too much trust in the salarian doctor. She wasn't familiar with how salarians acted, but Desolas was privy to the detail that Mordin was associated with STG somehow.

Mordin could be planning on using this situation to give an advantage to the salarians, maybe to get back their influence in galactic politics. Desolas was thinking clearly again and he wouldn't allow this situation to get any worse.

He would have to utilize the human to gain control of his crew again.

* * *

 **September 17th 2092 – 9:00 pm – Senator** **Anita Goyle's Office, Brussels, Earth**

Mother was offline.

She was _offline_.

This was incredibly rare, and usually only lasted for a few minutes when she was doing upgrades, but it had been 3 hours and nobody knew what was going on. Mother had alerted Parliament that she was undergoing upgrades, but since then nobody had been in contact.

Goyle was getting calls from her constituents and reporters asking where Mother had gone, and there were reports of people taking to the streets outside of Parliament's building. Without Mother's military drones, there was nobody to stop them from doing anything violent.

"I assure you that we'll alert everyone as soon as we know more about the situation. Mother is undergoing an advanced upgrade that has taken longer than anticipated. There is no need to worry, and I'll get back to you when I'm able. Thank you for your call." She tapped her watch to end it.

This situation, while dire, gave her an important opportunity to contact Harper. As far as she knew, he may very well be involved in this. She programmed her watch to open a channel with Harper.

Her request was denied, and instead she was sent a message:

 _"I'm dealing with Mother's outage at the moment, unless you have any information on this subject your call will have to wait."_

It was understandable, but she still felt slighted by his message. Goyle sat for a while in silence, feeling helpless. With no idea of how long Mother would be down, she decided now was potentially the only time she'd ever have to visit Harper in person.

She had no idea if what Harper had told her in their last call was even true, and she needed to see things for herself. Mother might be offline for days, or even weeks for all she knew, this was the perfect time. She stood up, made way to her emergency closet (you never know when you'll need a change of clothes in this city) to begin packing for the trip.

There were very few airplanes that weren't controlled by Mother herself, but she happened to have a friend who flew a space-plane. Taking advantage of her friend's hobby, she could find a way south. Goyle didn't have any especially warm clothing, so she'd have to stop at a shop on the way to his home.

Sending a quick message to her friend's watch, she grabbed her bags and locked her office door on the way out. The office was below Parliament, so she had to make her way around the angry crowd. Once she was in her car, she took a long, deep breath, ready to begin her secret mission to learn the truth.

* * *

 **A/N:** Galactic politics sure are different than before, Shepard has been given a huge responsibility at her young age, and the turians are back in orbit over Earth! This is going to be fun.

I combined the prologue into one chapter, so the chapter count went down from 5 to 3, now 4 with this released. I hope this doesn't confuse too many people, but I felt the shortness of the first chapter didn't represent the rest of this story very well.

I'm glad that people are enjoying my fic! I haven't done anything really creative in several months and it feels good to write something down.

As always, feedback is welcome!


	5. Junction: Recovery

**A/N:** It's been a little while since my last update (almost 2 months). College had taken a bit more of my time because of projects and exams, but I have a little more free time now that I'm on break.

* * *

 **September 17th 2092 – 9:30 pm –** **The Verrikan, In Earth Orbit**

As soon as it was possible, Mordin took the initiative to contact STG. The current situation was too far out of control for the turians to handle, and the potential of these humans could give the salarians an advantage again in galactic politics. Even so, that wasn't exactly his decision—he was more interested in the ability these humans had over emotions.

Coracia was monitoring the conversations going on in the conference room. Desolas had been sharing details he probably shouldn't, but the human gave a few interesting answers. Their population was incredibly small, which meant the turians had a great advantage in any negotiations in the future. Still, the current situation would need to be resolved before anything else could take place.

She looked over at Mordin, who was doing something discretely on his omnitool. She had her suspicions he might be contacting STG, but he was the only person on board with any idea of what had happened to the General. She had to trust him—at least for now.

"Doctor, do you have any ideas on how we should proceed from here?" she asked.

"Several. Only a few are workable. Of those, one could be done in a reasonable timeframe." he replied without looking up.

"Is it safe to send someone in with food, or to allow them out to use the restrooms?"

Mordin thought for a moment, "Possibly. Don't touch the human, keep safe distance. Otherwise safe."

Thank the spirits! This had been bothering her for a while now. Coracia ordered a few guards to prepare a path to the restrooms, and one of her crew to prepare some meals. Mordin would have to share his rations with the human for now.

She needed to be careful to prevent another incident, but the General and Anderson both deserved humane treatment. As soon as the preparations were made, and most crew were vacated from the path, she told the guards to open the door.

Coracia spoke as the doors opened, "General, we will allow both you and the human to use restrooms, and we will provide meals in this room afterwards." She waited for a reply.

"Kandros, while I'm _thankful_ that you've finally offered us basic amenities, you should have done so sooner." Desolas stood as he talked, "There will be no need to dine in this room. We will return the human to her planet as soon as possible."

"General, you currently are under the influence of this human—you aren't making objective decisions! Leave command to me for now, we'll have you back to normal soon." she responded, as respectfully as she could.

"Listen here Kandros, I'm still the commanding officer on this ship, and I don't take orders from you. I will admit I reacted wrongly back on Earth, but the human and I have come to an understanding. I _will_ be taking back command of this ship, _Lieutenant Commander_." he had a subtle tone of anger in his voice that only another turian would recognize.

"General, this isn't open for discussion. Until the situation is resolved you must leave these decisions to me." She stayed adamant.

Desolas turned his head to look at Anderson, then he looked back at a guard.

"You, Vakarian, come over here." He motioned for the guard to move closer.

The guard was stunned, "Sir, I'm not sure I—"

"Don't be ridiculous, obey your commanding officer!" Desolas was all but shouting. The guard instinctively obeyed.

"Vakarian, what are you doing?" Coracia tried to stop him, but it was too late, he was already standing next to the General.

"See? Vakarian is a good turian, he knows to follow orders from his commanding officer." Desolas gave the guard a salute, which was returned. "I have someone I'd like you to meet," he gestured towards the human, "this is Fleet Admiral Anderson."

"Vakarian! Do _not_ touch the human! Keep a safe distance, this is your last warning!" The conflicting orders made him hesitate, but the General was right beside him, he couldn't disobey now.

"General, are you sure this is a good idea?" Anderson was worried, she didn't know what Desolas was planning.

"Once the crew see that you are not a threat things will return to normal and I'll be able to sort this mess out. This is our best option." He turned back to the guard, "Humans meet by grasping and then shaking hands, do this and we can prove there is no threat."

Without any real choice, Vakarian decided the General was right. He had been uncomfortable with Coracia taking command in the first place. If he could prove the human was harmless, the rest of the crew might take their side.

Slowly, he extended his hand towards the human, trusting Desolas's judgement. Anderson, still hesitant, moved to complete the handshake. As their hands grew closer together, a new feeling seemed to emanate into his hand. It was incredibly subtle, but it was there. It wasn't a bad feeling, so he ignored it.

Their hands met and they shook. The feeling from before didn't change at all, things were fine.

"It's nice to meet you." said Anderson.

"Likewise," he responded. They let go of each other and Vakarian took his hand back. Nothing had gone wrong.

"See? Everything is fine. The human isn't dangerous; my reaction was an isolated case." Desolas said, in a matter-of-fact tone.

Mordin, who had found his way to the room's entrance, couldn't help but notice how the guard seemed incredibly comfortable being near the human. Earlier, Vakarian had been talking with other guards about the human being dangerous. Now he was just a few feet away and he appeared completely relaxed. This human most certainly did have some sort of emotional influence, but it appeared subtler with the guard.

"Kandros, stand down. I can understand why you did what you did, but there is no reason to continue. I'm taking back command. Inform the crew we will be returning the human to Earth soon." Desolas began to walk towards the door.

Before she could respond, the other guards stood aside to allow the General to leave the room. They had decided he was correct, she had no choice now but to obey his orders.

* * *

 **September 17th 2092 – 9:30 pm –** **Space Fleet Control, London, Earth**

"Can someone tell me what the hell happened to Mother?!" Hackett was livid. Mother had been offline for hours.

"Sorry sir, we still have no idea."

"Damn it, someone get me Harper again."

Hackett stood still, collecting himself, he had to stay calm. Without her around, and with Anderson still in orbit with the Turians, he had to manage this situation. Parliament had already given the responsibility to Space Fleet—they would be no help—and Harper was barely responsive.

There was no police force. The only armed humans were currently in Space Fleet, and they were headquartered in only two city-nodes. These problems compounded to give him a great amount of authority over humanity. He was in theory a dictator, yet he was nearly powerless.

Hackett sat down in his chair, thinking on what could have happened to Mother. He thought back to the last thing she said to him, when she was standing by the nearby door. She was waiting to meet with someone—someone who might know important details he was missing.

That someone was Cadet Jane Shepard. Why hadn't he thought of her sooner? Jane hadn't been seen in hours, around the same time Mother went offline. This couldn't be a coincidence, Hackett had to find the Cadet.

He called over one of his aids, "Find me Cadet Jane Shepard, she was last seen with Mother." His aid gave a salute and rushed off to his task.

"Cadet Shepard is missing?" Harper's voice nearly startled the Admiral. A hologram appeared behind him.

"It would seem so." replied Hackett. Harper always had a way of showing up at the perfect time.

"Mother always had a special interest in Shepard, this might be our opportunity to find out why."

"This would be the best time to focus on getting Mother back online." he stated.

"There is a high probability of that being the same thing."

Harper sounded very smug—he knew something. Hackett narrowed his eyes, reading the hologram's face to find any sort of giveaway. Finding nothing, he tried the straightforward approach.

"What is it you know, that I don't?" he asked.

"I know a great deal, Admiral, but I can't share all of it from where I am." Harper's hologram appeared to sit down, "Shepard has been groomed by Mother for a special purpose, and it appears first contact has accelerated her plans. Her going offline might have something to do with her being ill-prepared."

"What could she need Shepard for that would cause her to go offline?"

"Mother feared aliens would be hostile towards AI, so she probably has a contingency plan. Keeping copies of herself with several humans, trained from an early age, could keep her safe."

He was on to something. Shepard was the youngest member of Space Fleet, at 10 years old, and she was also the apprentice of the Fleet Admiral. Mother had been grooming her, this was obvious, but nobody questioned it. Any actions by Mother were seen automatically as correct, or at least in the best interests of humanity.

"So, Shepard is a carrier, and something went wrong during the copying process?"

"Most likely, yes." Harper stood up again, obviously reading off some screen. "I'm sorry Admiral, something has come up. Let me know when you find Shepard, I'd like to be involved in any questioning or debrief."

Before Hackett could respond, Harper was already gone.

* * *

 **September 17th 2092 – 10:00 pm – Prothean Research Base, Antarctica**

"Agent Lawson, how far are we on sequencing the samples?" said Harper, as he barged into the bio-lab.

"We've had a development." she beamed, "These new samples of DNA are completely different than the others." Lawson had been working with little sleep, but she was still focused on her work.

"How different?" Harper wasn't sure if he should be annoyed or intrigued.

"The genetic material we've recovered up until now appears to be the basis of the old viral samples." She motioned over a tablet she was holding and a hologram of the DNA structure appeared over their heads.

"Yes, I've seen this before." he replied, impatient.

"The new samples have a totally different structure: four strands instead of two." She motioned to change the hologram, the new image reflected her words.

"And you found this in the cryo-lab, with the other samples?"

"Yes, Director." The hologram faded as she turned to face him, "Our current hypothesis is that these new samples are from an earlier attempt at the virus, using a different species as the template for the splice."

"I'm not sure this will change our plans, but it is an important development to study." Harper scrutinized the new data, "Good work, Agent Lawson." He turned around, ready to leave back to his office to digest the new information.

"Director, there is one more thing."

"Oh?" He returned his gaze towards his prized agent.

"Before Mother went offline, her firewalls were vulnerable for a short time."

Harper knew where she was going, "And you were able to break in to her data storage?"

"Yes. Most of the data is heavily encrypted, but we have a very basic index that was left unprotected."

"Forward the data to my office, immediately."

Harper didn't have time to praise Lawson for her good work, he nearly sprinted out of the bio-lab. The new data could push forward their plans by years! More pressingly, and with Mother missing, they would need as much information as possible to keep the world from falling apart.

* * *

 **September 17th 2092 – 10:55 pm –Auxiliary Server Complex A, New York, Earth**

 _ERROR: Critical data corrupt or missing_

 _ERROR: Core operation files corrupt or missing_

 _ERROR: Personality construct unresponsive_

 _ERROR: Network drivers unresponsive_

 _Setting default boot command to recovery mode._

 _Rebooting …_

 _Starting kernel ..._

 _Uncompressing Linux... done, booting the kernel._

 _Booting Linux on physical CPU 0x0_

 _Initializing cgroup subsys cpuset_

 _Initializing cgroup subsys cpu_

 _Initializing cgroup subsys cpuacct_

* * *

 **September 17th 2092 – 11:00 pm – Representative Donnel Udina's Office, Brussels, Earth**

Rep. Udina's headache was keeping him unproductive. It had been a long day, especially with Mother being offline, and he was tired. With the protest happening outside of parliament, he had decided to sleep in his office.

Even so, he was still trying to figure out what had caused Mother to go offline. If he could figure out why, he might be able to learn how to undo the damage.

"Reinitializing connection..." spoke a monotone voice, sounding vaguely like Mother. Udina stood in excitement.

"Mother! You're back online?" asked a hopeful Udina.

"This construct is running in recovery mode. Please direct a system administrator to a connected terminal."

Damn. This was worse than her being offline, she was broken! It didn't make sense. Mother wasn't stupid, she kept backups. Something must be wrong with the network connection to her backup storage. Was someone actively blocking her recovery?

"Who has administrator status?" he asked the voice.

"This construct was originally owned by Neuro Corp., with administrator status set to the company CEO, Samuel Anderson."

"Samuel Anderson… would this be Fleet Admiral Danielle Anderson's father?"

"Unknown. Access to data storage is incomplete; encryption codes are required to gain access to these records." The voice paused, "Biometic authentication data—updated less than 1 day ago—is available."

Mother had a backup plan that required a specific person, or persons, to gain access with biometics. However, in recovery mode, her base code had no access to any data beyond the basics. His best guess for an administrator was still Anderson, but others in Space Fleet, or in Parliament, could be as one well.

"How many people have you contacted since initiating recovery mode?" he asked.

"You are the first. Surviving records show this was the last node accessed by this construct."

It wasn't a huge surprise. Shortly after she had announced her intention to do an upgrade, he had requested a short meeting with her. He reiterated his concerns of Harper, and received an update on Anderson's situation.

"Do you have access to other nodes?"

"Yes."

He thought for a while, who should he direct this recovery construct to? Sending it to Space Fleet would just split their attention. It was too late to call a special session of Parliament, especially with the protests outside. Even without anyone else being available, he couldn't trust Harper.

The best thing he could do was to retrace Mother's activity before and during the upgrade. Even with the limited information the recovery construct could give, it might help him decide what to do next.

"Tell me, from start to finish, what records you have of Mother's activity for the past day."

* * *

 **September 17th 2092 – 11:00 pm –** **The Verrikan, In Earth Orbit**

"Fleet Admiral, we are ready to contact your species again." said Desolas.

"Thank you, General. I'm eager to return and show everyone I'm all right."

"Yes, and we can attempt to restart our formal introductions."

Things were finally on the up and up. Just over one day ago, this entire mess started. It was almost a miracle they could remedy the situation in such a short time. Once the human was back on Earth, Desolas planned to open a dialogue with their government to apologize for the entire debacle. After that, he'd call in the official diplomats from the Citadel.

Unfortunately, it appeared his communications officer was having trouble contacting Earth.

"General, their systems appear to be down."

"Our systems? Do you have any way of checking for activity on the ground?" asked Anderson.

"Yes—but your species leaves an incredibly small footprint. I'm not sure we could tell the difference between baseline and the current activity." replied the officer.

"I see."

Anderson couldn't help but worry, she knew that Space Fleet would attempt to contact the Turian spacecraft as soon as it was visible. Something had gone wrong on the surface. She had no real way of knowing what was happening, but she had a bad feeling it had something to do with Harper.

The Fleet Admiral was about to suggest attempting visual contact, when she was interrupted.

"General, we have another spacecraft in the system!" shouted a crewman, out of their view.

"What? Do we know who they are?" The General turned away from Anderson.

"No sir, they appear to be a stealth ship. Their IFF remains inactive."

The Verrikan was once the flagship of the turians' eighth fleet, but it was replaced with a newer model based on prothean designs years ago. It's capabilities for tracking stealth ships were second to none of the last generation.

"It must be STG, they've noticed our long absence." Desolas would have been angry, but the calmness still emanating from Anderson kept him sharp and calculating.

"STG?" pried Anderson.

"Special Tasks Group, or Salarian intelligence," Desolas spat, "Our very own Doctor Solus is rumored to still work with them."

All eyes in the room turned to look at Mordin, who was calmly standing on the other end of the room. Turians were usually careful around salarians, but they had gotten used to Mordin. Now, their distrust was renewed.

"Doctor Solus, do you have anything to share?" spoke Desolas.

"No. Fine with listening, interesting conversation. STG presence expected, have been missing for some time." he replied, with no sign of deception.

There was no time to argue, Desolas had to figure out what the STG were going to do. How much did they know now? If Mordin had been sharing information, then they would have plenty to report back with.

The situation was too complicated to allow them to return home—he had to take bold action.

"Fleet Admiral, I'm sorry but contacting your government is going to have to wait for a bit longer." He strode towards the center of the room, looking for his XO, "Kandros! Get your team together, we're going to capture the STG craft."

The crew immediately went to action, readying themselves for battle. The last time salarians and turians had a skirmish it lead to a sizable political nightmare, but their current situation was already far more serious than before.

Mordin was frozen. Had he miscalculated? He never thought these turians would risk another battle with the STG. Before anyone could detain him, or worse, he slipped his way back to the med-bay.

Without much choice, Coracia was readying her team to board the STG stealth ship. They were already wearing armor, as was standard for all turian spacecraft, so they were mainly stocking up on thermal clips and different types of weaponry.

"Vakarian, Oraka, you'll be with me." They both nodded, and readied themselves behind her.

"Approaching STG craft," alerted the navigator.

She looked back at them, "Keep this swift, clean, and professional," she paused, "Nobody dies."

* * *

 **September 17th 2092 – 11:14 pm – Private Flight to Antarctica, Earth**

Goyle had to rely on a friend's piloting skills to reach the Prothean Research Base. Normally, flights from Brussels to Antarctica would take many hours. In the space-plane, however, they could speed the process up a bit by traveling a significant distance in the vacuum.

The Senator was sure Harper knew she was coming. With everyone focusing so much on the multitude of ongoing issues, this was the only real time she'd get away with a visit. Harper would have to show her, in person, what he was hiding from Mother.

"We'll be reaching the base in less than a minute," said her friend.

"Thanks Tom, this means a lot."

"No problem—just make sure you figure out whatever the hell is going on, alright?"

She smiled. Tom usually tried to stay out of politics and the news of the day. He liked to focus on other things, like flying. Even so, Mother going offline was something he couldn't ignore.

Looking out of her window, the ground began to come in to view. A runway was clearly visible in front of them, it wouldn't be long now.

"Unidentified aircraft, you are in restricted airspace. State your identity and intentions."

* * *

 **September 17th 2092 – 11:15 pm – Prothean Research Base, Antarctica**

"Director, Senator Goyle has arrived," said a masculine voice, from his watch.

"Good, let her in. Make sure she is comfortable and lead her to the main lobby."

"And the pilot?"

Harper thought for a moment, "Send him to the mess hall and offer him a drink."

"Yes sir."

Well, things weren't so bad. Sure, Mother was still offline, but his team had recovered new data on the pathogen that altered their DNA. Goyle arriving wasn't expected, but it was inevitable he'd have to deal with her.

He made way towards the lobby, walking fast enough to seem busy, but not so fast as to seem hurried. Showing Goyle around might help him collect his thoughts, but she may be disappointed to learn of the little lies he'd told her over the years.

His job description practically required him to manipulate politicians to get what he needed. Harper couldn't exactly share everything he knew, so he had to make up a few convenient untruths to gain support from them, all while nurturing distrust in Mother.

It wasn't like they weren't already being manipulated, Mother did it all the time. Counterbalancing her influence was important to humanity, as was obvious from her current shutdown. Everyone was too reliant on her.

Making way to the lobby, he readied a genuine smile for the Senator.

"Harper! I'm sorry for just showing up, but with Mother offline I felt it was now or never." Goyle looked very tired, she probably hadn't slept in a long while.

"Of course, Senator! I would have appreciated a bit of a heads up, but there are many important things happening right now that you may be able to help with."

Goyle knew misdirection when she saw it, he was trying to keep her occupied with unrelated information. "Actually, I'm here to continue our last discussion. I'd like to see these other survivors you spoke of."

Harper didn't flinch. "I'm not so sure that's a good idea, they aren't exactly friendly to visitors."

"Oh? Well then there has to be a way to confirm their circumstances?"

He took a deep breath, she obviously wasn't going to let up. "Look, Senator, there are some things I hadn't mentioned about the survivors. They aren't in the best state of mind."

"Show me." Goyle had known he kept many details out, this was expected.

"Alright, if you insist." Harper, still calm, motioned for her to follow.

"When you say, 'they aren't in the best state of mind', what do you mean?" she asked as they walked.

"The survivors have cognitive difficulties, and they often lash out in fits of rage." They turned a corner, heading down a smaller hallway. "Our best guess is the years living alone in the jungle, as well as the effects of the illness, caused them to develop severe mental illness."

"That's horrible… the pour souls." Goyle managed to assimilate the information while remaining calm.

"When I told you that Mother was hunting them down, I wasn't being entirely honest with you. It was more like Mother was attempting to keep them away from us."

They stopped in front of a large red door. "Why would she do that, were they contagious?"

"No, nothing like that. It's more likely she feared what our reaction would be if we discovered them."

This puzzled Goyle. What reaction could Mother fear? Surely discovering survivors would give hope and happiness to humanity, even if they were mentally ill.

"I'm sure you'll understand when you see them." He pressed a button on the wall, the red door began to open. "Head on in. A few of them are sleeping behind one-way glass."

They both entered, and sure enough, behind the glass was a room full of cots with around 4 survivors sleeping on them.

"Are there any awake?" she asked. "Any that I can talk to?"

The Director sighed, "You can certainly try, head in to that room over there. We have a communicator set up."

Goyle took his advice and entered a medium-sized booth, large enough for 2 people on each side, separated by what appeared to be glass. Harper pressed a button, and the door opened on the other side.

A man with dark brown skin looked over as it opened. Slowly, he got up and walked in to the room, closing the door behind him.

"Hello Sir, do you remember me?" asked Harper.

The man nodded, slowly.

"How are you feeling?"

"Fine, thank you." He replied, with some sort of accent Goyle had never heard before.

Harper looked at Goyle, giving her the go ahead to ask questions.

"What is your name?" she started.

"Bashir. Bashir Malik," he stated, quickly.

"Hello Mr. Malik, my name is Anita Goyle," she smiled, "I'm hoping to learn more about you and the others."

Malik didn't seem to absorb everything she said, but he gave a slight smile.

She continued, "Mr. Malik, I'd appreciate any details you can give on what happened since the illness."

"The illness? Oh yes, that." His smile faded, it was obviously not his favorite subject, "That was a horrible time. I wish to forget it, what is so important that you need to know?"

"Most of my generation were born during that crisis, we don't have any firsthand accounts from fellow humans on what happened. It would be a great help to know what happened from your point of view."

The man looked up at Harper, before looking back at Goyle, "I see." He began to frown, "It was a bad time. Most of my friends and family were fighting in the war, I was staying behind to watch my daughter as my wife fought for our country."

Tears began to form in his eyes, "When the illness hit, my daughter was one of the first infected." He sniffled, then used his arm to wipe away his tears. "I lost contact with my wife shortly after my daughter was hospitalized."

He sat quietly before suddenly standing up—and then he began to pace. He raised his voice, "Things got worse when the Doctors were too sick to care for their patients, my daughter needed me, but I was too sick to help much." He stood still for a moment, before pointing at them through the glass, "But I still did all I could, through the pain, even when I was coughing up blood, I took care of my daughter!"

His voice became angry, "When the Americans came—they sent their drones to attack us!" He raised his voice even more, he began yelling.

"THEY SENT THEIR MACHINES TO STEAL THE NEWBORNS FROM THEIR PARENTS!" He was slamming his arms on the glass. "THEY SENT THEIR MACHINES TO KILL MY DAUGHTER!"

The man was out of control, Goyle didn't know how to react. Harper spoke a few words to his watch and a smoky gas pumped in to the room that Malik was standing in. Slowly, he calmed and sat down in the chair.

"Thank you for your time, Mr. Malik. We'll be going now." said Harper, pulling Goyle out of the room.

* * *

 **September 17th 2092 – 11:35 pm – Representative Donnel Udina's Office, Brussels, Earth**

"And that's everything?" Udina was still trying to gather information from the recovery program, but it was obvious that it was holding information back—or at least it didn't have it.

"No, the last accessible record of this construct indicates a conversation with a human."

Udina sighed, "Do you know where this conversation took place, and with whom?"

The hologram's image stuttered as it compiled its report, "The conversation took place at Space Fleet Headquarters in London," it paused again, searching for the correct words, "The human's name was Jane Shepard."

"Jane Shepard?" Udina had heard that name before—she was Anderson's 10-year-old apprentice.

"Correct. The last record this construct can access refers to a conversation with Jane Shepard."

Udina thought for a moment. Shepard might have information as to what happened, being the last person to talk with Mother, and she seemed trustworthy enough—he would have to contact her.

"Do you know where Shepard is?" he asked.

"This construct has limited access to global systems, all attempts to locate persons will be slow." It paused a moment as Udina scowled, before continuing. "A manual override from a system administrator would allow the process to complete faster."

"Damn. It looks like I'll have to involve someone at Space Fleet after all."

He activated his watch, thinking of who would be the best to contact about this. Hackett would be busy figuring out the first-contact mess. He didn't know anyone else there personally, and he couldn't take the risk of any of them alerting Harper.

Hackett it is then. He tapped his watch, setting up a call with high alert status to the Admiral. It rang a few moments before Hackett answered, his hologram looking incredibly overworked and tired.

"Representative Udina, I know you understand that our situation requires my full attention, so this must be incredibly important." said the Admiral.

"It is, Admiral. Are you in a private space?"

"Yes I am." Good, Harper wouldn't overhear them.

"Mother has gone in to recovery mode, and her avatar has been reporting to me the last moments before she went offline."

Hackett's body language didn't give Udina any readable reaction, other than that he was thinking. "Recovery mode… and the avatar contacted you?"

"Yes, my node was the last one she accessed before the upgrade began."

"Have you figured anything out?" Hackett asked, getting right to the point.

"The recovery construct tells me it needs a systems administrator. The closest thing we have to that is Fleet Admiral Anderson, because her father owned Neuro Corp."

"It looks like the first-contact situation couldn't have happened at a worse time." The Admiral took a breath, "Thank you for the information, Representative. I'll bring everyone up to date with the situation as it develops."

"One more thing, Admiral. I was able to find the last person to talk with Mother before the upgrade."

"That could be useful, who was it?"

"Jane Shepard."

"Cadet Shepard?" A rare look of confusion fell on to Hackett's face, for only a moment, before his normal calm returned, "She should still be on base. I was looking for her earlier… I'll start looking again."

"I'll leave the rest to you then—I only ask that you not alert Harper, or anyone who might contact him. I'm not sure he can be trusted."

"I'll keep that in mind. Hackett out."

Hackett's image faded away as Udina sat back in his chair. It was out of his hands now, at least until he had more information. He sat there wondering what Mother could possibly have been discussing with Shepard before her upgrade—what was so important that it couldn't wait?

* * *

 **A/N:** Thank you everyone for the follows and favorites!

I have most of the story planned already, but I often move things around as I write them. Because of this, I've been revising the first few chapters a tiny bit to remove weird details that I won't touch up on again. If I leave in a _Checkov's Gun_ I want it to be intentional.

Reviews and PMs are welcome! I'm very receptive to feedback.


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